Oh, How the Times are Changing – Automation in the Clinical Microbiology Lab


Robotic specimen lines and huge machines are staples in the hematology and chemistry laboratories. At various MLS/clinical laboratory conventions, when we could attend those, all the major medical equipment companies were eager to debut their new analyzers. They would flaunt all the great new features trying to entice the laboratory administrators to buy. The analyzers that were always missing in this cacophony of wares were the microbiology analyzers. Hematology and chemistry are constantly changing, but if a tech who retired 30 years ago would walk into a micro lab today, it would be relatively the same with a few exceptions. Why is this? The truth is like microbiology – the answer is complicated.

This blog post will examine the past, present, and future of automation in the microbiology laboratory. It will also cover why automation has been slow to catch on in the micro lab and how it can be beneficial.


I would like to start out this section by begging for forgiveness, as I started working in the laboratory in 2010. Much of this information is based on interviews and stories from more experienced coworkers. I tried to be as accurate as possible with my information.

This section will focus on how microbiological organisms used to be identified and the arduous processes that were used. The descriptions will be brief, as the main focus will be primarily on automation.

Individual Biochemical Tests

Several different biochemical tests were set up in individual reaction test tubes using bacterial agar slants containing an inoculum of bacteria. These tests were incubated for a few hours to a few days. Reactions would then be recorded on a worksheet and the organism ID would be deduced on the basis of these reactions.

ID Kits/Biochemical Test Strips

ID kits and biochemical test strips were a step above the biochemical reactions. Essentially, the ID kits and test strips operated on the same principle as the biochemical reactions. The kits consisted of a strip of small reaction chambers that were inoculated with a bacterial suspension. The reaction strip was incubated either several hours or overnight and, after incubation, any supplemental reagents were added. The reactions were recorded on a worksheet and a numerical code was generated based on the positive reactions. This code was then checked in a reference book or entered in a computer database to determine the organism ID. Some of these ID kits and/or biochemical test strips may still be used in some small or remote laboratories.

Manual Antibiotic Susceptibility Testing

Sensitivities for organisms could be done in one of two ways:

Kirby Bauer: A lawn of bacteria is made on a Mueller Hinton agar plate using a bacterial suspension. Disks impregnated with antibiotics are placed on the agar plate and the plate is placed in an incubator overnight. The next day the zone of inhibition around the antibiotic disks is measured. The bacteria is deemed sensitive or resistant to a particular drug based on this zone. Kirby Bauer produces a qualitative result only, meaning it tells the clinician if a bacterium is sensitive or resistant to an antibiotic.

MIC Broth Dilution: This is when an inoculum of bacteria is introduced to successively higher concentrations of an antibiotic broth. The broth is incubated overnight and the next day the test tubes are observed for growth. The minimal inhibitory concentration (MIC) is the lowest concentration of antibiotic that will inhibit bacterial growth. This process takes several steps and requires many test tubes, however, it does offer a quantitative result allowing the physician to monitor antibiotic resistance.

Manual Plating of Blood Cultures

Blood cultures were initially plated and gram stained upon receipt to check for bacterial growth. The bottles were then incubated for four (4) days. On day four of incubation, the bottles were re-gram stained and re-plated to double check that none were positive. Any plates exhibiting growth were worked up for bacterial identification and antibiotic susceptibility testing.


This section describes the current processes for most microbiology labs and the limited automation that is currently in use. While much better than the older methods, automation in the micro lab has not really changed that much in the last 30 or so years.

Continuous Blood Culture Monitoring

Rather than gram staining and plating what could be hundreds of blood culture bottles, automated continuous monitoring blood culture instruments do a lot of the work for the tech. The blood culture bottles contain a fluorescent dye that reacts with the CO2 the bacteria produce. This dye emits a signal, the blood culture instrument reads this signal and alerts the technologist that there is a positive blood culture. The tech then removes the bottle from the instrument, plates the blood culture, makes and reads the gram stain, enters the results into the laboratory information system (LIS), and calls the value to the clinician. These instruments can be interfaced with the LIS and negative blood cultures can be updated at set intervals. This saves the technologist time and prevents the technologist from performing menial tasks. The technologist can devote more of their time to positive cultures.

Automated Microbial ID and Sensitivity Instrumentation

There are several different types of automated ID and sensitivity instruments on the market. Essentially, they all work the same way. Once the tech makes the appropriate suspension of the bacterial isolate and inoculates the ID-MIC panel, these automated instruments incubate, add all required supplemental reagents, and read all biochemical reactions and MIC values. They allow for much easier setup and quicker identification of the bacteria. These instruments perform all the same biochemical tests that a technologist would have to set up individually. The instrument uses an online database to compute the ID based on the positive and negative reactions.

Rapid ID Molecular Instrumentation

Rapid ID molecular instruments are normally used for stat testing, which would include flu, strep A, SARS-CoV-2 (COVID-19), among others. Some platforms have even introduced rapid ID of things like CREs, MRSA, and VREs. This shortens the time of ID from days or weeks in the case of viral cultures.


This section will explain some newer technologies. These are currently in use in some of the larger laboratories but are not yet commonplace in smaller laboratories.

Automated Specimen Processors

These analyzers plate the incoming microbiology specimens. The instrument is programmable to set what kind of plates to use for a particular culture and what kind of streaking pattern should be used. These instruments use liquid media into which the patient samples are inoculated. These tubes are loaded onto the instrument either capped or uncapped depending on the instrument. The instrument pipettes a drop of the liquid in the tube onto the preprogrammed agar plates for that particular culture. The instrument has a bar code reader that scans the specimen label to know what kind of culture it is. Once the plates areis inoculated, the instrument streaks the plates, moves the plates to the off rack, and sorts them by culture type. The technologist can then remove these plates and place them into the incubator.

Total Laboratory Automation Instruments

These instruments process the specimens, incubate the specimens, read the plates, and store records of past patient histories. They often have an open architecture meaning incubator and processing sections can be added and removed as needed. After processing specimens, the instrument then loads the plates into incubators, reads the plates at intervals updating the no growth plates in the LIS, and alerting the technologist of positive plates that need attention. This type of system records images of the plates allowing the technologist to look at patient histories and compare current bacterial growth to past bacterial growth. Right now it is not currently possible to load positive plates directly onto an ID/sensitivity instrument, however, some companies are trying to develop this.

How Can Automation Help?

There are many benefits to automating the microbiology laboratory. Microbiology requires extensive manual labor. Each culture has to be looked at individually and updated one by one. This means that there is a lot of redundant work and a lot of time spent on cultures that are not clinically significant.

Staffing Shortages

The medical laboratory field is extremely short-staffed and laboratories are always trying to figure out how to do more with less. An automatic plating instrument would eliminate the need for techs to perform this work. Depending on the size of the lab, this could free up anywhere between 1-5 techs. This means that these techs can focus on actual patient testing and culture workup.

Time Saver

Automation will help alleviate some of the redundant work. For example, automatic plate readers will automatically read and update no growth plates in the LIS, freeing the techs so they can then spend more time with positive cultures.

Boost Productivity

Automation could allow for more work to go on after hours. In smaller labs, micro is usually not 24/7. This means that any specimens received after closing time would not be processed until the next day, delaying patient results by almost a full 24 hours. With an automatic processor, a tech from another department or a specimen processing associate could load the specimens onto the instrument for plating. The inoculated specimen plates would then be incubating overnight and would be ready for workup the next day. Results could also be sent out during off-hours and cultures that were no growth could be updated sooner due to automatic plate reading.

Why has Automation in Microbiology Been Slow to Catch On?

Let’s look at some of the reasons why automation hasn’t caught on to the same degree as other areas of the lab.

Quality Concerns

Microbiology is a technical area. The technologist has to look at the cultures and interpret which bacteria are pathogens and which bacteria are normal flora from a particular site. There are a lot of little nuances. For example, alpha-hemolytic Strep generally isn’t worked up in sputum cultures unless it looks like Streptococcus pneuomoniae or it’s the only bacteria growing in the culture. Coagulase-negative Staph generally is not worked up in any cultures unless it’s a culture from a sterile site such as blood, body fluid, or tissue, or urine from a woman of child-bearing age. Coag-negative Staph may be mentioned in the final report of a wound or sputum culture depending on how many other organisms are present, but the actual species is unimportant. All these little rules and exceptions would be incredibly difficult to program into an instrument and it is more efficient to have a human looking at the plates.

Other quality concerns include making sure that cultures are pure before loading into an ID/AST instrument. This means that a technologist may have to isolate a bacteria onto a separate agar plate before setting up for ID and sensitivity. If a mixed culture is used for ID, the two different bacterias can cross-react with each other and give an erroneous ID.

Lack of Specimen Standardization

This is probably one of the biggest roadblocks to implementing automation. Unlike chemistry and hematology where specimens come in a standardized tube, microbiology specimens can come on a swab, in a sterile container, a bottle, a test tube, and even Tupperware-like containers. It is very hard to build an instrument/analyzer that can accommodate all these different containers.


This is probably the other big roadblock. The current instruments/analyzers that are on the market are very expensive, costing several hundred thousand dollars. As it stands right now the only labs where it makes sense to have these types of analyzers are high-volume laboratories.


Automation takes up space. The analyzers need to be in a well-ventilated area, on a level surface, and can’t have a lot of debris around them. This may require remolding and rearranging of laboratory furniture. This is an arduous process and disrupts the technologists and workflow of the laboratory.


Microbiology is one of the more complicated areas of the laboratory and, therefore, it has been very hard to automate. Technology is becoming more affordable, smaller, and more advanced, making it a possibility that microbiology will soon be as automated as chemistry and hematology. Many people may worry that automation will cost jobs, however as it stands now, the laboratory field is experiencing a staffing shortage that is only going to get worse. Technology can help fill in the gaps where there used to be people. Soon the microbiology lab will be completely unrecognizable.

2 Replies to “Oh, How the Times are Changing – Automation in the Clinical Microbiology Lab”

    1. Hi Carol! Thanks so much for the positive feedback. Sara Zaucha is just one of our very talented and dedicated blog contributors. We have been so blessed to have lab professionals offer to volunteer their time to provide blog content for the website. We truly appreciate hearing from you. Thank you for continuing to follow our efforts to educate and advocate for the medical laboratory professions.

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