Automation in microbiology laboratory

Sh Nilica Devi *

While automation in other areas of clinical laboratory, more specifically in haematology and clinical chemistry, have moved on to automation in testing in a big way, microbiology has not been able to jump on to the automation bandwagon and has remained largely insulated from the trend happening across the laboratories.

Although there has been some degree of automation in microbiology laboratory, notably in continuous-monitoring blood culture systems, automated microbial identification, and automated antimicrobial susceptibility testing systems, important steps like microbiology specimen processing and culture workup, in particular, remain largely manual tasks. Not much change could be achieved in the way the methodsused to perform these tasks were done and they have remained more or less the same for many years.

Need for rapid microbiology testing: The field of infectious diseases is faced with dramatic changes everywhere. During the last few decades, we have seen the emergence of multidrug-resistant organisms, increase of international travel which result in easier spread of infectious agents between populations. This is compounded bythe demographic change happening across the globe, and the climate change.

The burden of infectious diseases is still very high and great amounts of morbidity and mortality worldwide are caused by infections. Due to increased travel by people and population exchanges, pathogens can move across populations with ease. This can lead to the introduction of pathogens or resistance genes in previously unaffected regions or populations.

This might also influence the growing prevalence rates of multidrug-resistant organisms, increased costs of antibiotic therapy, significant increased length of stay, and isolation costs. The most important factor fuelling the multidrug-resistant organisms epidemic is the extensive use of broad-spectrum antibiotics which triggers the proliferation of highly resistant organisms. To counter the menace, rapid microbiological testing is seen as being extremely necessary.

Longer result delivery with conventional methods: While there have been dramatic improvements in efficiency with conventional testing methods such as Gram staining, culture, phenotyping and susceptibility, the long waiting time to the final result is still a limiting factor.

On an average, routine microbiology testing can take anywhere from 48 to 72 hours till the final result delivery. This delay can result in incorrect antibiotic therapy, prevent early targeted therapy and can promote infections to more resistant organisms. Why has it taken until only recently for the microbiology laboratory to move towards total laboratory automation?

Microbiology is too complex to automate: In comparison to haematology and chemistry specimens, most of which are blood or urine based and use limited types of tubes, microbiology specimens are much more complex. Microbiology specimens include blood, body fluids, tissues, stool specimens, catheter tips, prosthetic devices, and lower respiratory tract specimens.

Further, microbiology specimens are transported by utilising a variety of devices that include urine transport tubes, swab collection devices, sterile containers for fluids and tissues, aspirates and sputum collection devices. An additional aspect of complexity of microbiology testing is the variation in the manner in which the specimens are processed.

New era of automation in microbiology: Challenged by the necessity to have faster turnaround times and with increase in microbiology test volumes in most laboratories, the need for automation has been felt for quite some time now. Automation would also allow the use of small specimen volume for accurate results.

With the advent of new innovations in computer technology and the system interfacing with Laboratory Information Systems (LIS), the possibility of transcription errors have been minimised significantly.

Automation in microbiology is taking place everywhere in bigger laboratories, and some of its benefits include:
o Less manual tasks: Automation gets rid of finding appropriate plates for each sample, physically moving plates to and from the incubator, putting in specimens, and other repetitive manual tasks.
o Traceability: Here, each plate has a complete electronic audit trail attached to it, including when it was inoculated, incubated and read, and by whom.
o Better plate spreading: Automated spreading facilitates the use of the whole agar plate and improved isolation of single colonies.
o Less chances of contamination: As the manual handling gets minimised, the chances of the specimens getting contaminated is significantly reduced.
o Incubation times are standardised: Automation allows pre-set incubation times, and hence, pre-set plate reading times. It does away with the conventional concept of Day 1 or Day 2 reading. This means, faster turnaround times.
o Automated plate interpretation: New technologies are able to process rapid detection of plates with no growth and plates with colonies of a particular colour.
o Storage of digital images: Images of plates could be stored to be viewed again at any stage in the future.
o Remote reading and checking: The system would allow the plate images to be checked or read from anywhere via the internet. It also allows for double checking or second opinion from microbiologists anywhere.

Emerging technologies: Among the new automation trends in microbiology, the most significant are the liquid-based systems and matrix-assisted laser desorption ionisation – time of flight (MALDI-TOF). In the former, liquid-based transportsystem enables inoculation of the specimen and smear preparation with automated liquid-based specimen processors.

In the latter, the technology allows accurate, fast and inexpensive identification of microorganisms isolated from clinical specimens. The procedure is highly favourable for automation because they are technically relatively simple and reproducible.

Conclusion: The field of microbiology testing is undergoing a sea change at the moment and we’ll be seeing more automation in this area in the near-future. Automation is needed not merely from the operational point of view but from the accuracy and reliability of test results as well. With rapid automation delivering results in shorter time, it is a huge advantage for the patients as well.