The advent of digital microbiology

March 19, 2015

Full laboratory automation and digital Microbiology are trending topics high on a lot of laboratories’ list. The increase in interest in this technology is mostly driven by, in Dr. Novak and Dr. Marlowe’s summation, “budget cuts, shrinking workforce, and legislation-mandated testing,”1 as well as increasing pressure to maintain quality. VanBelkum, et al., note that “culture has been the mainstay of clinical microbiology for the past century and will likely remain so for decades to come,”2 but because of current pressures and its manual nature, clinical microbiology is experiencing unprecedented changes and evolving at a rapid pace.

Europe seemed to have taken the lead with implementation of full laboratory automation, but 2014 marked the year of its adoption in clinical microbiology laboratories by pioneers in the United States and Canada. During 2014, different manufacturers’ systems of the new generation of full laboratory automation and digital Microbiology were installed in North American laboratories. The modular and open full laboratory automation systems for Microbiology consist of front-end specimen processors that automatically seed cultures, prepare Gram slides for staining, and inoculate broths, with a conveyor track connecting the processors to smart incubators which include image acquisition stations that gather the images needed for downstream digital Microbiology analysis. So, what are some of the early benefits and process improvements that these automated lines are bringing to laboratories across North America?

Smart incubators and faster growth

A key component of the new full laboratory automation in Microbiology is the use of smart incubators, which place each individual plate on its own shelf. The initial rationale for individual shelves inside the smart incubators is mainly for random and faster retrieval when the laboratory professional wishes to access a particular plate. However, one interesting benefit of the smart incubators is that cultures grow faster in them as compared to traditional incubators, and therefore cultures are ready to be read sooner. The reason for the faster growth is that each culture plate is placed on its own shelf inside the incubator, which provides for a homogeneous atmosphere and efficient thermal conductivity in the incubator to bring the culture plate up to optimal conditions faster. Because the smart incubators are not constantly being opened, they are able to maintain those optimal conditions uninterruptedly.3 As this incubation technology is implemented, Microbiologists and clinicians will be able to work together to select the optimal reading time to benefit from faster growth with faster turnaround times for reports.

Image acquisition stations and streamlined analysis

The image acquisition stations built into the full laboratory automation systems use highly sophisticated cameras and versatile lighting systems to obtain sharp, unparalleled high-resolution images (Figure 1).The high quality of the images acquired by the system enables laboratorians to zoom in on the culture plates and to detect even small colonies that could be obscured or potentially be hard to see. One manufacturer has pioneered discriminative image analysis software that uses the plate image taken at time 0, and compares it to the images taken after incubation. The software is able to discriminate artifacts present on the plate at time 0, focus on the growth, and recognize even small colonies. The software groups the plates according to the estimated number of colonies, and the system then sorts the plates from most estimated colonies to least estimated colonies and presents them to the laboratory professional for interpretation and analysis. The laboratorians can then decide which plates represent significant growth and choose to work these up first.

Figure 1. Comparison of plate photo taken with professional camera (A) to image captured using trilinear image acquisition station camera (B)

This new technology helps speed up the workup of positive cultures, by presenting them to the operator first, and leaving the no-growth cultures for last. In the case of no-growth cultures, the laboratory professional, after reviewing the plates, can result them in groups, without having to manually discard the plates. It is important to emphasize that the new systems do not make the decisions for the laboratory personnel; the software simplifies and groups culture plates for faster interpretation and increased operational efficiencies.

Digital records and remote image sharing

Bringing the laboratory back to the patient’s bedside is an important benefit of digital microbiology. With laboratory consolidation, often the laboratory is no longer close to the patient bedside. If a physician wants to go to the laboratory for consultation and to discuss a result, it is no longer possible to walk down the hall and speak to Microbiology personnel. Digital microbiology allows the laboratory to share the image of a culture plate and/or of the Gram stain with the physician, who may be in a remote location. This is a practice currently used in some European laboratories that have adopted full lab automation of the Microbiology laboratory. Laboratory personnel can provide key patient information and consultation to clinicians faster to expedite patient treatment and improve care.

Standardization and rationalization

A downstream indirect benefit of full laboratory automation in Microbiology is the standardization and rationalization of sample containers. A few years ago, the concept of liquid-based Microbiology seemed distant and unnecessary. In fact, Microbiology, unlike Chemistry and Hematology, was used to receiving a buffet of sample types in different sizes and containers.

The adoption of automated specimen processing technology, however, is driving laboratories to standardize and rationalize the containers they receive to optimize the use of the automated processors. When laboratories adopt full laboratory automation, MacKenzie notes, they “define which specimens are to be included and stratify which have the highest priority (i.e., screening, routine swabs, respiratory secretions, stools, etc.),”4 to be able to roll out the implementation in stages starting from the highest sample volume with the highest negativity rates. Automated specimen processors are able to handle non-liquid samples, but in order to maximize the use of the processors, Microbiology laboratories are optimizing workflow by standardizing containers, such as vacuum tubes for urines, elution swabs, and sputum liquefying containers, among others. Standardization of sample collection devices benefits clinicians by simplifying and reducing the number of specimen containers needed at specimen collection sites. In fact, Fontana, et al., assert that liquid-based Microbiology “allows clinical specimen optimization and has several important advantages: cost reduction (due to the smaller number of different devices used), time savings for medical or nursing staff (less confusion in collection device selection and fewer samples being collected), time savings for laboratory staff (fewer samples to access and handle for individual investigations), and patient comfort improvement (multiple sample collection can be avoided).”5

Faster colony growth, grouping culture plates by estimated number of colonies for streamlined analysis, providing clinicians with digital patient records with images of cultures and Gram stains for clinical actionable results faster, and laboratory standardization are early buzz-worthy benefits of full laboratory automation and digital Microbiology. As more and more laboratories in North America embrace this new technology, the benefits in terms of faster turnaround times, better patient care, and the relevance of traditional culture will be substantial.


  1. Novak SM, Marlowe EM. “Automation in the Clinical Microbiology Laboratory.” Clin Lab Med. 2013;33: 567–588.
  2. vanBelkum A, Durand G, Peyret M, et al. Rapid clinical bacteriology and its future impact. Ann Lab Med. 2013;33(1):14-27. doi: 10.3343/alm.2013.33.1.14. Epub 2012 Dec 17.
  3. Thomson RB.Total Automation in Today’s Clinical Microbiology Laboratory: A Buyer’s Perspective. In Advanced for the Administrators of the Laboratory Webinar Series.
  4. MacKenzie CR. Usefulness of automatisation in a university diagnostic laboratory: more than meets the eyeDGHM Congress, Berlin December 2011.  Retrieved 1/15/15. Accessed February 4, 2015.
  5. Fontana C, Favaro M, Cartesio F. “How liquid based microbiology can change the workflow in the microbiology laboratories.” Advances in Microbiology, 2013, 3, 504-510 Published online October 2013. Accessed February 6, 2015.