Recent refinement in technology has resulted in more user-friendly automated testing platforms that have lowered risk for contamination, decreased costs, and are faster than older platforms.
Timely identification of infectious agents and early introduction of an appropriate antimicrobial therapy is crucial in clinical practice, particularly in severe infections. Surveillance and early detection of antimicrobial resistant strains should be the priority of the diagnostic microbiology as resistant bacteria are involved into hospital outbreaks as well as in sepsis. Particularly during an outbreak, the impact of rapid diagnostics can be substantial and directly influence infection control and treatment options as well as having a strong positive financial impact on healthcare. Traditional microbiologic methods remain suboptimal in providing rapid identification and susceptibility testing. There is a growing need for more rapid and reliable laboratory results. Important progress made in the fields of instruments, reagents, and techniques have made it easier to adapt to the important changes of the clinical microbiology context e.g. increasing use of microbiology tests, shortage of qualified personnel.
When it comes to automation, clinical microbiology has for many years lagged behind other laboratory disciplines. Robotics and computer processing revolutionized chemistry and hematology instruments decades ago. However, clinical microbiology has now incorporated on its routine a lot of automated methods, which allowed the increase in performance of several tests in a short time, reduced the number of technical errors, and introduced huge software possibilities of data analysis. Interestingly most of the microbiology technology used at this moment involves automatization of the conventional manual procedures. The microbiology processes are becoming increasingly more complex. Informatics is playing an increasing role in the improvement of these processes in terms of workflow, timeliness, and cost. Recent refinements in technology have resulted in more user-friendly automated testing platforms that have lowered risks for contamination, decreased costs, and are faster than older platforms. Total laboratory automation systems currently available handle specimens, streak plates, incubate, and digitally image cultures. There have been more changes and more advances in the last few years than there have been for decades.
There is a constant need to upgrade the existing technologies and develop innovative new technologies for better, safer, and faster diagnosis of diseases. Currently, there are several innovative approaches that are developed and are still under development for rapid antimicrobial susceptibility testing (AST) aimed at faster detection times and reduced sample processing for effortless integration into a clinical lab setting.
Forward laser light scatter technology. FLLS is one of the emerging technologies for early determination of AST. This system uses a laser light source to measure the concentration of particles in the liquid samples (optical density – OD) as well as the scattered intensity in a direction near to the laser beam. The system can be used to run up to 16 samples simultaneously, with measurements done automatically every 3 minutes for accurate density change measurements. This was initially developed for urinalysis and now has been adapted to be used for AST. Using this technology, the system can obtain results in about 6 hours for fast growing microorganisms and can take up to 18 hours for slower growing organisms. The system is accurate and has potential to replace the existing microdilution systems and is not limited by the use of probes or markers.
Human robot collaboration in clinical microbiology. Collaborating robots is a latest technology for full laboratory automation. In an age of increasing workloads and diminishing resources, various tasks can be performed by robotic systems, while highly qualified laboratory professional can focus on esoteric tasks that require their experience, knowledge, and training. The new robotic system 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. Technologists simply scan the specimen barcode, and the robot presents the precise sequence of pre-labeled plates or tubes. After the plates are manually seeded, the robot streaks the plates and places them on the conveyor track to incubators. The robot can also be used to automatically seed MALDI-TOF slides and set up AST/ID panels. Using this robot, one can improve traceability and reduce transcription and transposition errors in the manual processes.
Automated plate assessment system. Traditional laboratory processes for the preparation and analysis of culture plates involve microbiologists manually examining each specimen and separating out those that need further attention. This can be a time-consuming process, which has implications for doctors and patients waiting on results, and consume critical resources. This is even truer in a country like ours where microbiologists are in short supply. APAS is an artificial intelligence technology for the automated imaging, image analysis, interpretation, and reporting of growth on microbiology plates after incubation. It helps to improve the diagnostic efficiency of microbiology laboratories and enables faster reporting of infectious diseases. The instrument successfully triages negative plates out of the workflow, allowing microbiologists to focus on positive plates only. In addition, the APAS facilitates significant upstream benefits in specimen processing.
Next-generation sequencing. Clinical microbiology laboratories help to lessen the burden of infectious disease by detecting and characterizing pathogens in infected patients or those pathogens circulating in the community. In this scenario, implementation of NGS can potentially assist in clinical and public health decisions by determining the causative agent of infectious disease and/or the epidemiology and evolution of various infecting pathogens in the hospital or community settings. With its multitude of benefits, NGS is becoming the gold standard in bacteriology; however, since it is not yet fully accessible (particularly in low resource settings), currently NGS is mainly used at a level of reference microbiology rather than routine.
With the rapid advances in NGS technologies and capabilities, clinical microbiologists are recognizing that the influence of NGS on the diagnostic cycle will be in the scale of a disruptive technology, potentially reducing the time from diagnosis to clinical treatment, while also reducing the requirement for wet laboratory-based analyses performed in tandem. It is particularly important in outbreak detection and monitoring the evolution and dynamics of multi-drug resistant pathogens. Consequently, NGS should become routine in the clinical microbiology laboratory. However, further studies are required to improve the workflow for NGS, by shortening the turnaround time for the library preparation and the runs on the NGS platforms, and further reducing costs.
Mass spectrometry. MS was successfully introduced as a new diagnostic gold standard method in clinical microbiology for rapid, accurate, and cost-effective microbial species identification. The introduction of matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) MS for routine identification of microbial pathogens has profoundly influenced microbiological diagnostics, and is progressively replacing biochemical identification methods. MALDI-TOF MS technology has been shown to be a suitable tool for high throughput and complete automation in clinical microbiology laboratory. Recently, a semi-quantitative MALDI-TOF MS-based method for the detection of antibiotic resistance was developed. This assay allows rapid identification and susceptibility testing of both Gram negative and Gram-positive pathogens in a single assay within approximately 3-4 hours. The assay is also applicable for AST directly from blood culture fluid with high sensitivity, specificity, and an overall accuracy rate of 95 percent.
Subsequent developments have mainly focused on software and database improvements, making MALDI-TOF MS an increasingly robust and accurate tool for microbial identification. However, application of MALDI-TOF MS for rapid susceptibility testing or epidemiological studies is currently hampered by the lack of standardized protocols, test kits, and software tools. Furthermore, laboratory equipment is expensive and in need of costly maintenance although the operating costs are low.
Systems are emerging for the clinical microbiology laboratory with the potential to automate almost all areas of testing. The manufacturers have already piloted modules that will pick colonies from plates, send samples to mass spectrometry for identification, put up a suspension for susceptibility testing, and read the results. Laboratories that can afford to automate are likely to recover their costs, especially as added features lead to more efficiency. While early adopters of automation had to make the business case based on labor savings, now there are many more reasons to justify the change economically. The fact that the industry is advancing technologies like digital imaging really makes the business case much easier.
The possibility of real-time testing tools would not only help to save lives but would also have the potential to enable targeted antibiotic treatment at disease onset, potentially slowing the evolution of antibiotic resistance and improving antibiotic stewardship. Given the ever-increasing spread of antibiotic resistance, researchers much develop innovative technologies, which could allow rapid microbiological diagnostic within an hour, to be applied to samples collected directly from the patient, either of sterile or contaminated biological products. As a result, the workflow in the microbiology laboratory will change at a rapid pace and microbiologists will have the challenge of selecting the most appropriate, clinically useful, and cost-effective automation for their laboratories.
Changing Trends In Microbiology
Microbiology is an ever-changing field. Over the last few years, microbiology labs changed from following discrete manual processes to fully automated systems, which include the pre-analytical phase of processing, gram staining, culture including automated blood culture systems, identification, and sensitivity of microorganisms. Now with the rise in viral infections like swine flu and Ebola across the world, nucleic acid tests will replace the viral culture and serology will become obsolete in the near future.
Although selected nucleic acid-based tests have replaced a number of traditional bacteriology tests, the vast majority of these provide complementary information to traditional culture-based tests. Multiplex nucleic acid-based tests and arrays and MALDI-TOF technologies and applications are rapidly evolving and will inevitably have a significant effect on our ability to offer prompt and effective antimicrobial therapy to our patients.
The advantage of molecular diagnostics is to detect any disease at an initial stage of development. On the other hand, not all labs can afford such costly molecular tests. Our country’s laboratories are under increasing pressure to save money, resulting in the need for inexpensive, yet effective, rapid microbiology tests. Automated microbiology is fast, but the costs per test, and initial capital investment are quite high. The research in microbiology should focus on fast, easy-to-use, rapid tests for bacterial, viral, and parasitic pathogens such as multidrug resistant organisms. Thus, a faster turnaround time (TAT) and immediate results are the major factors that will drive the microbiology market.
Another important factor to be considered is to use biological reference materials that are authentic, traceable, and reliable to ensure the quality control of tests being performed. The need of the hour is to combine advanced IT solutions like artificial intelligence and nanotechnology with the existing diagnostic technologies to develop rapid, cost-effective tests which can be easily interpreted and made available across the entire country.
Dr Anu Gupta
Lab Head and Microbiologist,
Head – Infection Control,
Fortis Escorts Heart Institute