Automation in Clinical Microbiology


Historically, the trend toward automation in clinical pathology laboratories has largely bypassed the clinical microbiology laboratory. In this article, we review the historical impediments to automation in the microbiology laboratory and offer insight into the reasons why we believe that we are on the cusp of a dramatic change that will sweep a wave of automation into clinical microbiology laboratories. We review the currently available specimen-processing instruments as well as the total laboratory automation solutions. Lastly, we outline the types of studies that will need to be performed to fully assess the benefits of automation in microbiology laboratories.


In recent years, while automation has steadily spread throughout the clinical chemistry and clinical hematology areas of diagnostic laboratories, clinical microbiology laboratories have largely been excluded from this trend. Although continuous-monitoring blood culture systems, automated microbial identification, and automated antimicrobial susceptibility testing systems are widely utilized in microbiology laboratories, microbiology specimen processing and culture workup, in particular, remain largely manual tasks, and indeed, few changes to the methods used to perform these tasks have occurred for many years. While we acknowledge that some larger microbiology laboratories utilize urine-plating instrumentation, most microbiology laboratories have little to- no automation in their specimen-processing areas, with the exception of some laboratories in Western Europe, Australia, and the Middle Eastern nations. Still fewer laboratories have implemented some version of total laboratory automation (TLA).

Driven by a variety of factors, we believe that the level and degree of automation in clinical microbiology laboratories are poised for a dramatic change. While it would probably be an overstatement to suggest that a tsunami of automation is sweeping toward microbiology laboratories, we do believe it accurate to state that a wave of automation is coming to microbiology laboratories and that this change will occur much more rapidly than most laboratorians may suspect; moreover, the changes associated with selection and implementation of microbiology automation solutions will place significant management and financial challenges upon laboratory leadership. Of the primary drivers of automation, standardization of identification methods to matrix assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) and the adoption of liquid microbiology specimen transport have allowed microbiology laboratories to simplify collection and identification systems, creating a work flow that can be optimized with automation.

For the purposes of this article, the use of the term “automation” in clinical microbiology laboratories excludes blood culture systems, automated microbial identification systems, and automated antimicrobial susceptibility testing systems; rather, it refers specifically to microbiology specimen-processing instruments and microbiology TLA solutions.

In this article, we review historical impediments to implementation of automation in microbiology laboratories and discuss the reasons why we believe that attitudes toward automation are changing. In addition, we review each of the currently available microbiology processing instruments and total microbiology automation solutions.


Several real or perceived factors have contributed to the current dearth of automation in clinical microbiology labs. These include the ideas that microbiology is too complex to automate, no machine can replace a human in the microbiology laboratory, automation is too expensive for microbiology laboratories, and microbiology laboratories are too small to automate.