In microbiology, where rapid turnaround times are critical for the treatment of life-threatening infections, total laboratory automation is the future to increase efficiency and reduce time to obtain results.
The growing burden of infectious diseases in India is amongst the highest worldwide. Rapid reporting of microbiology culture results is of utmost importance in the management of infectious diseases and is essential for patient care. Clinical microbiology as a science is evolving on a daily basis with new technology being developed rapidly. In the past decade, clinical microbiology has experienced revolutionary advances in terms of culture-independent molecular detection assays, laboratory automation, information systems linkage, and point-of-care testing, to name but a few. These new innovative diagnostic tools have resulted in major clinical impact by reducing the time to obtain results.
Still, today’s microbiology labs face unprecedented challenges. They are forced to do more with less by processing rising specimen volumes due to lab consolidations, while they experience a shortage of skilled lab technicians, and increasing cost pressures. Many new innovative diagnostic approaches have been made available during the last 10 years with a major impact on patient care and public health surveillance. Laboratories must adapt in an environment with evolving standards and available technologies. For example, rapid diagnostics assays, be it chromatography-based assays or the molecular assays help in better management; molecular methods based on nucleic acid detection or the use of proteomics have better sensitivity and specificity over chromatography assays.
Although a relatively new concept in clinical microbiology, total laboratory automation (TLA) has been successfully implemented and utilized in the clinical chemistry and hematology laboratories. In microbiology, where rapid turnaround times are critical for the treatment of life-threatening infections, partial automation has been successfully implemented for blood culture and mycobacterial culture systems. New technological advances in automation and a projected shortage of skilled laboratory technologists have further prompted the development of solutions for microbiology laboratory automation.
It appears logical that TLA would be able to reduce turnaround time and increase efficiency in the microbiology labs.
With the advent of technology in IVD, the field of clinical microbiology is evolving everyday with the test methods and the techniques to that extent that the test results are available as early as 2 hours with minimal interference and best report outcome.
MALDI-TOF MS. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has revolutionized organism identification in the clinical microbiology laboratory. The development of MALDI-TOF MS has made it possible to apply MS to infectious disease diagnostics applications, and MS is now being used for rapid identification of pathogens following cell culture. Compared to biochemical methods of identification that require further bacterial growth and incubation, MALDI-TOF MS is able to identify bacterial species more quickly and accurately and at a lower cost.
Advances in molecular microbiology. Molecular diagnostics for infectious disease testing offers one of the brightest areas for growth and innovation. Novel technologies continue to emerge, significantly reducing the time it takes to diagnose infectious diseases. Until recently, sequencing applications in microbiology have been limited. This is starting to change. At this time, next generation sequencing (NGS) based tests are mostly laboratory developed tests for oncology or genetic testing. However, companies are starting to apply NGS to infectious disease diagnostics.
The use of an available high-throughput whole genome sequencing (WGS) platform forms an additional advantage. Outsourced WGS analysis of human pathogens has been recently shown to be portable for supporting multi-state outbreak investigations. Real-time monitoring of multidrug-resistant organisms (MDROs) using WGS provides unprecedented resolution, dynamic population genetics, and precise actionable results against resistant organisms in a healthcare setting.
FISH. Fluorescence in situ hybridization (FISH) is one of the rapid methods for easy identification of microbial pathogens, and diagnosis of pathogens in human infections in the laboratory diagnostic routine. As a microscopic technique, FISH has the potential to provide information about spatial resolution, morphology, and identification of key pathogens in mixed species samples. Ongoing automation and commercialization of the FISH procedure have led to significant shortening of the time-to-result and increased test reliability.
Automation. Lab automation is helping to transform the microbiology lab workflow by automating plate selection, barcoding, inoculation, streaking, transportation, incubation, and imaging. Microbiology lab automation technologies automate time consuming, error prone, and manual tasks in order to increase lab efficiency, helping labs to provide higher quality and more accurate results faster, while the lab processes a higher volume of samples altogether. Digital images allow lab technicians and microbiologists to review plates anytime, anywhere, including remote locations and offer the ability to build algorithms that can automatically provide results without human intervention.
Informatics. Informatics tools enable seamless connectivity between the laboratory information system (LIS) and other lab instruments helping labs to create an integrated workflow with a single user interface and provide laboratorians with access to real-time data and analytics. Cloud-based informatics systems also allow data to be aggregated across labs from the same network, helping with performance benchmarking, analysis, and standardization of protocols. Modern informatics systems ensure that the latest data privacy and cyber security requirements are met, while providing on-demand access to information, reports, and analytics which can improve lab productivity, reduce errors, and shorten time to results.
Antimicrobial resistance (AMR) is a growing concern in India, with several government initiatives beginning to fund R&D in this space, for instance the government has notified governance mechanisms to develop a National Action Plan for AMR and to oversee AMR containment activities. The Ministry of Health and Family Welfare is constantly engaged in activities for containment of AMR in the country. Laboratories have been able to initiate data reporting system in WHONET, the software for AMR surveillance data reporting. Labs have also been assessed for building capacity toward quality testing. Given the cross-disciplinary and multi-faceted nature of AMR, it is and will likely remain a grand challenge for India
However, laboratory automation in clinical microbiology has the potential to revolutionize laboratory operations. A number of laboratories have automated part or most of their work and found that testing can be performed accurately, with reduced turnaround times, improvements in laboratory efficiency, and increased flexibility in the level of skill required to perform work in the laboratory. Even highly complex tasks such as visual interpretation of Gram stains, of culture results, and of susceptibility tests can be automated. Use of TLA has the potential to allow staff to perform more-complex tasks that will take advantage of their expertise. The recent launch of COPAN’s new Collaborative Robot in the United States of America is a step forward for full laboratory automation. The Collaborative Robot, with applied robotics and use of artificial intelligence, automatically manages many manual microbiology processes done at the laboratory bench, such as processing traditional fiber swabs, positive blood culture bottles, tissues, wound aspirates, and sterile body fluids.
As it is well-known that new microorganisms are being discovered all the time and they are developing more and more resistance to antibiotics, hence microbiologists aim at the application of different microbes for the betterment of human health. Prospective buyers opt for automated rapid diagnostic instruments which have a small footprint as space always remains a constraint to a laboratory. Availability of bidirectional interfacing and a user-friendly interface are other essential aspects of such instruments for a buyer. The future of clinical microbiology will be improved detection of all pathogens including new ones with rapidity and reduced cost making them reach the smallest market for improved infectious disease diagnostics.
Ever Changing Requirement Of Microbiology Labs
Microbiology is an ever expending branch in laboratory diagnosis, not only in terms of variety of investigation that it serves but also techniques that are being incorporated to improve the accuracy of results. In last few decades, the focus is on the replacement of conventional techniques by automation. Development of kit-based rapid techniques is a major achievement in last three decades. As the techniques are ever changing the requirement of equipment and reagents also changes accordingly. One of the major challenges in establishment of a new microbiology laboratory is the type of equipment to be installed. To make this job easy for medical colleges and also to regulate the quality of work, the Medical Council of India has specified a list of minimum number and type of equipment that must be there in the microbiology setup. A microbiologist may refer to this document published in Part III, Section 4 of the Gazette of India dated April 29, 1999 to set up a private laboratory with changes according to his needs.
A laboratory can perform a number of investigations by conventional techniques. It can further add to services by providing kit-based rapid tests. However the current trend is to establish an automation system for further expansion of the laboratory. Several equipment are now available that support automation in microbiology such as:
- An automated system for blood culture and some other samples that reduce turnaround time for isolation of bacterial isolate from blood. Separate systems are also available for culture of Mycobacteial tuberculosis from sputum samples;
- Automated system for identification and susceptibility which gives multiparametric identification with isolate profiles and TRUE MIC values for AST; and
- An automated, continuous monitoring mycobacterial culture system is recognized as the gold standard for TB diagnosis as well as first line and second line drug susceptibility testing.
Dr Harmesh Manocha
Associate Professor and HOD,
Department of Microbiology,
Government Institute of Medical Sciences