Winds of Change

A wave of automation is being felt by clinical microbiology laboratories and this change will occur much more rapidly than most microbiologists expect.

Microbiology as a science has expanded by leaps and bounds in the past few decades due to advancements in sophisticated instrumentation and recombinant DNA technology, which have added new dimension and revealed the understanding of the subject at molecular level. This has resulted in the emergence of several applications of this domain. The market is rapidly growing due to the increasing adoption of automated and advanced technologies for laboratory instruments and analyzers in developed countries. Growing geriatric population, and thereby rising prevalence of infectious diseases, is one of the major factors boosting the adoption of clinical microbiology in healthcare sector for disease diagnosis and monitoring. In addition, the industry is gaining high momentum with launch of innovative products such as MALDI Biotyper, GeneXpert, and Myla IT performance management solutions. Moreover, with the US FDA approving the Xpert Carba-R, commercialization of clinical microbiology devices is expected to increase significantly over the next few years.

Market Dynamics
The global clinical microbiology market was valued at USD 9 billion in 2016 and is expected to reach a value of USD 16.1 billion by 2024. Key factors driving the market growth include constant introduction of advanced products, coupled with increasing demand in pharmaceutical and clinical applications for investigation, and diagnosis of various infectious diseases.

Reagents segment is the largest segment with market share of 34.7 percent in 2016. With rapid adoption of technology and automation of laboratory workflow, laboratory instrument segment is expected to be the fastest growing segment with CAGR of 8.6 percent.

In 2016, North America dominated the global market with largest revenue share of 41 percent. The continuous research on infectious disease treatment and subsequent grant from government healthcare agencies are contributing to the development of a strong ecosystem for the expansion of clinical microbiology in the region.

Asia-Pacific is expected to emerge as the fastest-growing region in the period 2016–2024. The growing geriatric population in India, China, and Japan leading to increase in the prevalence of re-emerging infectious diseases, such as tuberculosis, cholera, and typhoid in this region, are expected to promote the clinical application of microbiology in healthcare.

The market is presently dominated by bioMerieux S.A., Cepheid Inc., Danaher Corporation and Bruker Corporation. Some of the prominent players operating in the market include Becton Dickinson & Company, Hologic Inc., Roche Diagnostics, and Alere Inc. Introduction of automated systems and innovative designs is expected to intensify the competition by changing the market dynamics over the next 5 years.

Value Proposition for Full Laboratory Automation
The field of clinical microbiology is rapidly evolving because of several recent technological advances. From walk-away multiplex PCR assays to total laboratory automation, microbiologists are able to produce faster results of higher quality than ever before.

Several driving forces that are changing attitudes about automation in microbiology laboratories have emerged. These relate to overall changes in the laboratory industry, growing shortages of trained personnel, declining reimbursement, a growing demand for improved quality, and two very important technological innovations: the introduction of liquid-based swab transport devices and the emergence of MALDI-TOF technology.

Industry changes. Changes in the industry are multiple. Overall testing volumes are increasing 10 to 15 percent per year, driven in part by an aging population, testing innovations, infection control demands, and the growing challenges resulting from detection and identification of multidrug-resistant microorganisms. Consolidation of laboratories, particularly for microbiology testing, continues to increase. Larger laboratories have a greater potential to benefit from lab automation than smaller laboratories. The 24-h, 7-day/week (24/7) microbiology laboratory is becoming much more common, and automation that can shorten turnaround time is being viewed more favorably. The 24/7 microbiology laboratory also allows cultures to be read following an appropriate incubation time, rather than waiting for the day shift, a scientifically unnecessary delay which can result in delays in turnaround time. Today, in most laboratories, plate reading is primarily a first-shift activity. TLA will facilitate reading plates on other shifts as well. Lastly, relatively speaking, reimbursement is declining and opportunities for enhanced reimbursement in the current healthcare environment are low.

Personnel shortages. Although they have stabilized recently, shortages in trained microbiology technologists are an industry challenge. Fewer students are choosing medical technology as a career than a generation ago. Moreover, the number of medical technology training programs has been dramatically declining. The pay for medical technologists is also low compared to that of some other healthcare professionals. Each of these challenges has resulted in the mean age of the current workforce continuing to increase without sufficient replacement workers for those eligible for retirement.

Quality issues. Demand by clinicians for new tests continues to grow, not just in total numbers but also for the types (width and breadth) of testing being performed, driven in part by the clinical utility of many of the newer molecularly based assays for the diagnosis of infectious diseases. The trend toward decreasingly shorter lengths of stay for hospital inpatients has led to increased demand for more rapid turnaround times for infectious disease assays. While tests are sometimes less expensive when they are performed by a reference laboratory, the longer turnaround time for a reference lab test result drives the impetus to bring some of this testing back to hospital laboratories.

Another aspect of quality is the increasing importance placed on traceability for laboratory testing. Automated specimen processors and TLA solutions provide far greater traceability than when the same testing is performed manually.

Liquid-based microbiology. Traditionally, microbiology swabs have been transported in a device that was designed to keep a specimen associated with the swab during the transport period. The swab itself has been used to inoculate media and prepare smears. A paradigm shift occurred with the introduction of liquid-based swab transport devices, first with ESwab (Copan, Murrieta, CA) and later with other, similar products. With these products, the specimen is associated not with the swab but with the liquid phase of the transport device. The presence of the specimen in a liquid-based transport enables inoculation of the specimen and smear preparation with automated liquid-based specimen processors.

Full laboratory automation. For automation to be successful, it will need to be flexible in design, embrace the human element, and adapt to the challenges of specimen diversity. One important recent change that is hastening the adoption of full laboratory automation is the change in sample collection devices. Advances in collection devices, paired with liquid-based microbiology (LBM), developed in recent years, have improved sample quality and opened the door to automate front-end specimen processing, one of the most manual areas of the laboratory. In fact, the adoption of liquid microbiology specimen transport has allowed microbiology laboratories to simplify collection and identification systems, creating a workflow that can be optimized with automation.

Different pressures, such as increasing sample volume, aging workforce, and decreasing reimbursement, are making the concept of automation a pressing need for the laboratory. However, culture analysis is still a time-intensive and costly procedure for the laboratory as technologists have to interpret colony counts to differentiate pathogens from normal flora for several hundred plates a day. Software that can automatically segregate patients’ sample cultures based on colony counts and/or recognition of the specific morphology or appearance of the colonies will completely revolutionize the microbiology laboratory by saving time to results and improving the speed of diagnosis of infectious disease. Image analysis capabilities and the strength of the algorithms for automatic reading and segregation of cultures, regardless of the manufacturer of plated media, will separate the mechanization of manual processes from true game-changing innovation in image analysis in the field of full laboratory automation for microbiology, and will constitute the most important factor when choosing a system.

Reading Algorithms. The image analysis software is the most powerful component of full laboratory automation, and it is at the heart of digital microbiology. Without strong algorithms, the return on investment and the value of full laboratory automation are limited because a lot of the tasks still have to be done manually. It is important that the algorithms use an open approach to different media manufacturers and different types of media, and that they can be applied to both whole and bi-plates. Many laboratories in the US use bi-plates for urine investigations. So, availability of reading algorithms for bi-plates is an important feature to consider when picking a full laboratory automation system.

Urine is one of the highest sample volumes received in a microbiology laboratory. In fact, urinalysis is the third major diagnostic screening test in a clinical laboratory, only preceded by serum/plasma chemistry profiles and complete blood count analysis. The urine reading algorithm must be able to use the correct sample volume to get accurate colonial separation for an accurate account. It must also work on blood/MacConkey or blood/chromogenic medium, in addition to being able to recognize the orientation of the plates no matter which side of the plate is blood and which is the other medium. The bi-plate urine segregation algorithm applies the appropriate rules based on a customizable expert system of rules for growth interpretation. So, two automatic results can be received instantaneously from one culture plate. For example, by applying if and then rules, the system could flag if the patient is a pregnant woman or is of child-bearing age, then look for small numbers of white Group B Strep colonies on the chromogenic plates or look for small numbers of hemolytic colonies on blood plates.

What’s Next?
With the level of sophistication that lies behind current image analysis software, the next frontier for clinical microbiology is automated colony picking. The module for automated colony picking works using 3D digital coordinates previously specified by the laboratory staff to process further workup and investigations. The workups include McFarland suspensions for antibiotic susceptibility testing (AST) and traditional organism identification by biochemistry and purity plates, seeding MALDI-TOF target plates, and applying the matrix, among others.

As microbiology laboratories around the globe brace for this exciting new wave of automation, it is important for lab leaders to select a system that has the software capabilities necessary to automate internal processes and the power to considerably reduce turnaround times by pre-sorting samples to facilitate a lean workflow. It is an exciting time for microbiology – we are part of one of the largest breakthroughs in technology in this generation.

Way Ahead
Driven by a variety of factors, the level and degree of automation in clinical microbiology laboratories is poised for a dramatic change. While it would probably be an overstatement to suggest that a tsunami of automation is sweeping toward microbiology laboratories, it is accurate to state that a wave of automation is coming to microbiology laboratories and that this change will occur much more rapidly than most laboratory experts expect; moreover, the changes associated with selection and implementation of microbiology automation solutions will place significant management and financial challenges upon laboratory leadership. There is no doubt that the benefits of automation on laboratory efficiency and indirectly on clinical care will be profound.