The question frequently being asked is, “Can labs afford not to automate in a transformational environment, where consolidation is rampant?”
Clinical microbiology laboratories are undergoing a rapid transformation, with many of these changes posing daunting challenges. At a time when the complexity of diagnostic testing and associated costs are increasing, labs are experiencing reimbursement pressure from both government and commercial payers. These forces are driving laboratories to consolidate and move specimens to centralized facilities with the goal to improve testing efficiencies and decrease costs and turnaround time.
Laboratory consolidation also brings challenges. Testing is potentially moved away from physicians at a time when the interpretation of sophisticated tests requires active collaboration with the microbiology staff. Also, concentration of diagnostic procedures in large centralized laboratories poses increased safety risks for the technical staff at a time when infections with antimicrobial-resistant organisms and other communicable pathogens are increasing. One can accept these changes as inevitable problems or can view them from another perspective. Necessity is the mother of innovation, or to rephrase – when they give lemons, make lemonade. Today innovation – lemonade – is comprehensive automation from the specimen receipt to the transmission of the final report.
Automation in microbiology is not simply automating the traditional practices of processing specimens and incubating cultures – that would not be transformative. Automation should be viewed as an all-encompassing approach to processing samples and communicating information that enable laboratory technologists to perform skilled tasks in ways not historically possible. This is why automation was recently described as a paradigm shift in clinical microbiology, representing the beginning of the future.
Automation in microbiology enables laboratories to do much more than eliminate the manual repetitive practices and inefficiencies of the past – the laboratory noise. Realizing the full value of automation, however, means fundamentally reexamining the entire laboratory workflow.
Pandemic shifts the focus to infectious diseases
Dr. Rohini Kalhan
Alaknanda Diagnostic Lab
Today, what everyone is talking about and is aware of is COVID-19 or SARS Con V2, which is the cause of the pandemic of this century. This pandemic has taught many things and among them is the awareness of infectious diseases, especially viral diseases, which is the biggest threat to humanity in the coming years and decades. To counter this biggest threat to humanity, what is needed is early diagnosis and treatment and that requires molecular testing and antigen detection, followed by antibody detection. The need of the hour will be to have affordable and rapid molecular diagnostic solutions and rapid antigen and antibody detection kits for proper detection and management of viral and bacterial diseases.
There are numerous viral diseases, which cause severe diseases, and can be fatal like HIV, Hepatitis B and C, Ebola virus, as well as bacterial diseases, which can be diagnosed very early, if we have cost-effective and rapid molecular testing machines and kits, which even small and medium laboratories can afford. Another most important thing needed to be addressed is the increase in antibiotic resistance, for which we need antibiotic stewardship, i.e., when and where to use antibiotics judiciously. If we do not actively solve this issue, we may soon reach the pre-antibiotic era when we were not able to treat small infections like boils, and people used to die because of small common infections and post-surgical infections. To help in this decision of when and what antibiotics to use, we need to diagnose the infection and antibiotic susceptibility as early as possible to reduce the use of broad-spectrum antibiotics and unnecessary antibiotics, which are used in lots of viral infections, thinking of them as bacterial infections.
For this, we need automated or rapid culture, detection, and antibiotic susceptibility, affordable and available at the level of small and medium labs. In the last few decades, people had forgotten about infectious diseases, and were concentrating only on lifestyle diseases and malignancies, but this pandemic has shown that infectious diseases are one of the most dangerous and not to be taken lightly but be prepared for.
So be aware, be prepared, and stay safe!
Automation impacting the clinical microbiology lab
Automation has transformed clinical laboratory disciplines like chemistry and hematology, but has until recently left the microbiology space relatively untouched.
However, a combination of rising sample volumes, cost pressures, and staffing shortages, along with technological advances, has led to increasing uptake of automation by clinical microbiologists. And while the field has traditionally relied heavily on manual processes, at this point almost every step in a typical clinical bacteriology workflow can be automated.
Additionally, several firms are developing AI-based approaches to reading culture plates that could further streamline the process.
The move to automation is really taking place as a result of the challenges around the accessible supply of qualified technicians and scientists. Consolidation of microbiology labs is upping the sample volumes individual labs have to process, while at the same time reducing the number of facilities available to train new lab staff. On top of that, there is also the rise of antimicrobial resistance, which is increasing the complexity (of clinical microbiology). So, automation is a solution to a lot of those challenges. There are a number of companies offering partial automation systems covering various portions of the clinical microbiology workflow.
Microbiology automation systems can be broken down into three parts: specimen processors, which take samples arriving to the lab and streak them onto culture plates; incubators, where cultures are grown and monitored via digital imaging; and automated colony pickers, which take the bacterial colonies selected by the microbiologist as requiring following up and transferring them to, for instance, a MALDI plate for MALDI-TOF-based identification, or using them to prepare suspension fluids for antibiotic susceptibility testing.
These components replicate manual workflows that typically consist of a half-dozen or more touchpoints for lab staff. In the absence of automation, samples first have to be sorted and batched according to what kind of test will be run on them. Technicians then culture specimens on media plates that have to be handled and sorted, then incubated, and then sorted again based on what amount of growth is observed.
In a manual system, technicians have to go in and out of the incubator to check plates for growth, which disturbs growing conditions, leading to slower and less consistent growth. Additionally, plates are typically checked at a single point during a shift. This means that plates that went into the incubator late in one shift probably would not have incubated for long enough when the tech comes to check for growth and may have to wait until the following shift to come out.
Allowing techs to monitor plate growth remotely using digital imaging limits disturbances of the incubation conditions, while also providing more flexible timing around when to check plates – both factors that streamline the culturing process.
In specimen processing, improved efficiency and specimen traceability are achieved with automation. Specimens are processed without delay upon receipt in the laboratory, with the automated selection of appropriate media for individual specimens, labeling the plates with barcodes, and inoculation of the media before they are transported to incubators on track systems. The accuracy of specimen inoculation is facilitated with the use of calibrated pipettes, and streaking of multiple culture plates can be done simultaneously in a variety of patterns. For maximum benefits, workflow changes are required, including elimination of the practice of batching specimens, manual creation of worklists, and aligning work schedules with traditional daytime service hours. Additionally, automation challenges to think differently about traditional processes. To obtain isolated colonies and perform semi-quantitation, plates were streaked historically in a quadrant pattern. However, this is unnecessary because automation provides more uniform, reproducible plate streaking with more isolated colonies and accurate quantitation.
Full laboratory automation moves plates from the processing area to incubators, eliminating delays in incubation. The plates are incubated under ideal growth conditions of stable temperature and atmosphere because the doors are not opened, and growth is monitored through images taken by sophisticated camera systems at predetermined time periods. Thus, significant growth can be detected earlier, with improved recovery of both common and slow-growing pathogens.
Imaging algorithms are capable of creating idealized images that are more than simple photographs under different lighting conditions. These images are similar to what a photographer can create with advanced photo-processing software. Software also allows these images to be examined under increased magnification, so subtle differences in colony morphologies or the presence of mixed cultures can be recognized. However, interpreting these images is a new skill for technologists that must be mastered. To continue physically examining plates at a workbench that includes the art of the sights and smells of traditional microbiology, is to deny the benefits of the science that comes from automation.
Automation can provide a library of images for training purposes, or the images of an individual patient’s culture for discussion with a healthcare provider. Digital imaging allows a technologist to examine culture plates in a specialized reading room, at home, or remotely hundreds or thousands of miles away from where the culture is performed, enabling technologists to consult with peers or specialists as needed. Sophisticated imaging software can also determine if growth is present on a culture plate as well as the quantity of growth, thus permitting the technologist to concentrate on processing plates with significant microbial growth.
Automation also provides a level of safety never imagined. Techs do not have to handle most specimens with automated processing. Furthermore, since the steps of transferring culture plates to incubators, examination of cultures with digital imaging, and the automation of identification and antimicrobial susceptibility testing, it is conceivable that lab technologists may never have to handle a culture plate.
Despite the pressures driving increased automation in clinical microbiology, the space was unlikely to see major new entrants. The market has not saturated; yet, there is still a lot of potential for growth. However, it will be difficult to see this being a market where a lot of big players will come in, given the size of the market and that it is already at a pretty mature stage.
Clinical microbiology lab – Changing dynamics
Dr Anu Gupta
As our government has advised to upscale the microbiology labs at district level, this is a great opportunity for clinical microbiologists in this crisis. Over the next few years, microbiology labs might see a significant transformation from discrete manual processes to fully automated systems, which includes pre-analytical phase of processing, Gram staining, and culture, including automated blood culture systems, identification, and sensitivity of microorganisms.
New molecular methods like target amplification by different PCRs, gene sequencing, pyrosequencing, reverse hybridization, mass spectrometry, and microarray analysis help in fast and accurate identification of the causative pathogens (including viruses) as well as detection of associated resistance markers. MALDI-TOF MS (matrix-associated laser desorption/ionization-time of flight mass spectroscopy) is an analytical method used for the detection of proteins (fatty acids, metabolites of microorganisms, and oligo/polysaccharides) and DNA molecules. Its application in clinical microbiology laboratory is as an alternative to traditional identification systems and ELISAs and is commercially available in India. Point-of-care clinical microbiology also helps in real-time management of patients presenting with infectious-disease emergency (viruses/bacteria/fungi). Indian healthcare industry is a potential market in microbiology. With high prevalence of infectious diseases, development of antimicrobial resistance, aging of population resulting in rising incidences of cardiac and other diseases, and rapidly increasing awareness about disease diagnosis and prevention.
The economics of total lab automation
Finally, as labs look at total lab automation, the question that has frequently been asked is “Can labs afford it?” Clearly, automation is a significant investment, but the more appropriate question is “Can labs afford not to automate?”
In an era when laboratories have to reduce costs, improve efficiency and quality, and provide more timely, accurate results to inform patient management, automation is the only solution. Recently, researchers have demonstrated that they were able to reduce staffing for both processing specimens and working up cultures, decrease time-to-results and costs by performing fewer subcultures and earlier reading of cultures, and increase the number of specimens processed by each technologist by using automation to eliminate inefficiencies. In their model, researchers were able to demonstrate a return on investment in 3 years rather than their projected 5-year RoI through labor savings alone.
Yes, there is an initial investment in automation and the infrastructure to support automation. Successful implementation of automation requires changing traditional workflow processes. Strong leadership and teamwork will be needed through the transition. But the rewards are great – Improved efficiencies, more timely results for better patient management, and more cost-effective diagnostics. Automation truly is the future of clinical microbiology.