Advances in Microbiology Automation

Advances in Microbiology Automation

The clinical laboratory, whether it is hospital-based or part of a national reference network, has changed rapidly and significantly in the last 10 years. Perhaps more so than other health care departments, the laboratory was dependent on tedious and manual functions that could also be very repetitive. In the 1960s, the advent of reliable and efficient instruments to perform many of these tasks revolutionized the daily work of the laboratory, especially in chemistry and hematology. Multi-channel analyzers and cell counters were developed, methodologies continually improved and specimen quantity requirements decreased as accuracy and reliability of the instruments increased.


In the ’80s, laboratory finances faced a dramatic shift in focus. What had once been a “fee-per-test” arena that made the laboratory a revenue center was now governed by various reimbursement structures that changed the lab into a cost center. Charges were now regulated by “approved” and “medically necessary” diagnoses and more uniform test codes to prevent fraud and create more universally acknowledged testing patterns. Clearly, money-saving measures had to be quickly embraced so clinical laboratories could continue to function with decreased reimbursement. Added to this problem were two additional needs to be met:

1. a decrease in the turnaround time (TAT) per test and

2. an increase in continuous quality improvement (CQI).

Again, chemistry and hematology were able to respond and become more efficient as their instrumentation advanced and total automation technology was considered. As hospital partnerships were created and labs merged, the opportunity arose to look at the whole laboratory situation with a different perspective.

Real or artificial boundaries in the laboratory were dissolved and stat labs, rapid response areas and chematology were new terms describing more efficient functionalities. As the laboratory information system (LIS) became more sophisticated, conveyor systems equipped with LIS download information were designed to deliver specimens to workstations or work cells where an interfaced instrument directly sampled the specimen. The sample could then move on to another instrument for different testing or to an archival storage unit. After results were completed and verified, they could quickly be delivered to the physician via the LIS interface.

At this time LIS capabilities were also improving and interfaces to most popular diagnostic instruments became available. Accuracy of sampling and results verification became hallmarks of good automation systems and greatly reduced the human error factor.

Given the rapid response mechanism of a reliable and accurate automation system, the clinical laboratory was meeting decreased TAT demands as well as complying with aspects of CQI. And, with structures in place such as Diagnosis Related Groups (DRGs) that dictated payment format, money could be saved on a per test basis as test volume increased. Whether it’s defined as merely an instrument interfaced to a PC and LIS or a completely unattended system involving robotics and multiple interfaces, automation is here to stay.

Automation in Microbiology

The mid ’60s brought some changes to clinical microbiology, in particular. Identification kits became popular and the Kirby-Bauer system for determining antibiotic susceptibilities became the standard in most laboratories. The kits contained small cupules of media and indicators that reacted with cultured organisms. Identifications were still done manually by reading the biochemical reactions, much as had been done with the tubed media. The miniaturization of the media was an advancement—it saved inoculation time and space in the incubation area and freed up technologist time.

The success and acceptance of these new products led to the development, in the 1970s, of more automated identification systems using some of the same principles and techniques. Color reactions were the basis for two of the new analyzers, the AutoScan (Dade MicroScan, West Sacramento, CA) and Vitek (bioMérieux, Hazelwood, MO). The AutoScan instruments used 96 well plates for the miniaturized biochemicals (at first, frozen media, later lyophilized product was contained in each well) and the Vitek used plastic cards with a choice of a variety of wells with either conventional or more novel dried media.

Automated susceptibility systems were also a significant part of these instruments, using the principles of nephelometry, fluorometry and/or simple turbidity.

Laboratory technologists found, however, that their experience was still of immense value if the organism identification resulted by the instrument was incorrect. Quick visual assessment of results became the norm, but this was still saving time over completely manual methods.

Although each instrument required individual manual inoculation of the plates or cards, the organism identification and susceptibility was automatically calculated, printed as well as stored in a database.

In clinical microbiology, new and emerging infectious agents, coupled with the development of many new antibiotics, demanded that culture results be readily available for retrospective analysis and future epidemiological studies. Technology changes, novel infectious agents with multiple drug resistances and new antibiotics, however, created challenges.

Blood Culture Instrumentation

The changes in instrumentation and automation for basic culture needs have run a parallel course with the development of blood culture systems. The importance of septicemia detection to the clinician cannot be overstated. The very manual inoculation, incubation, reading and sampling of the bottles make this laboratory task both costly and prone to contamination. Automating blood cultures, therefore, has been gladly accepted by most microbiologists. In fact, many laboratories have moved the blood culture analyzer to the “rapid response” area in the re-engineered laboratory.

The BACTEC 460 (Becton-Dickinson Microbiology Systems [BDMS], Cockeysville, MD) was the original automated blood culture instrument, now accompanied by several other innovative instruments, including the BacT/ALERT (Organon Teknika, Durham, NC), ESP System II (Trek Diagnostic Systems Inc., Westlake, OH) and the BACTEC 9000 Series (BDMS). Each is unique in its own methodology, but all have moved toward the concept of a non-invasive system that does not necessitate the repeated subculture of negative bottles.

While the manipulation of bottles and handling of negative cultures has been reduced, the work-up of positive cultures remains largely a manual activity. Gram stain, subculture, identification and susceptibilities, for example, are all done on an as-needed basis. And while automating DNA probe assays directly from blood culture bottles has been on the microbiology wish list, there are no such developments yet.

Specimen Delivery

No section of the clinical laboratory receives a wider variety of specimens than microbiology. Not satisfied with tubes of whole blood to be centrifuged and separated, the microbiologist eagerly awaits urine, throat swabs, stools, sputum, cerebrospinal and other bodily fluids. And the containers can be as varied as the specimen type.

Total laboratory automation systems such as those from LAB-InterLink (Omaha, NE), Beckman/Coulter (Fullerton, CA) and MDS AutoLab (Etobicoke, Ontario, CA) support the use of tubes in specimen transport containers on a conveyor system. Adaptations to handle other specimen container types are being investigated; timely delivery of specimens to the microbiology section from the central receiving area of the lab would be very helpful. This is especially important if the microbiology area is not geographically adjacent to the main laboratory.

Automated guided vehicles (AGVs) are used in some laboratories to deliver specimens, including those for microbiology. The AGV usually has large drawer-like bins into which many different types of containers can be placed. Central processing personnel can load up an AGV and dispatch it along its guide path of reflective tape; it may be programmed to deliver all manner of specimen container types to cytology, histology, molecular diagnostics and microbiology.

Specimen Processing

Once the specimens reach microbiology for culture, the traditional manual plating area is still found in most laboratories where laboratorians inoculate a variety of solid and liquid media to enhance bacterial/viral/fungal growth. These steps are taken after an assessment is made of the suitability of the specimen for the test(s) ordered. This evaluation is not based on volume alone, but often requires experienced judgment as to quality of what has been sent to the laboratory.

Some facilities have made this function less manual by using an automated culture station, such as the InocuLAB from Dynacon Systems Inc., Ontario, Canada. Robotic arms perform the streaking action, allowing the instrument to handle a variety of specimens such as urines, throat and genital swabs, as well as a variety of media types. The automated streaking can be more precise and reproducible than that of the varying methods of different technologists, but use in small- to medium-sized labs will have to be considered.

Another significant advance in the automation of immediate handling of microbiology specimens is the Bactis 160US instrument (Combact Diagnostic Systems, Hertzliya, Israel). In use as a urine screening system, the Bactis US160 can identify positive specimens that require culture. The methodology consists of a microscopic imaging system, aided by computer assisted robotics, that can screen urine specimens for the presence and concentration of bacteria. Computer image analysis measures the optical properties of a monolayer of fluorescent-stained bacteria. The obvious advantage of screening out negative urines and foregoing costly culture techniques is of great interest, especially to large volume labs.

“The instrument is totally automated and results are available in about 30 minutes,”says Franklin R. Cockerill, MD, chairman of Microbiology and a consultant in Laboratory Medicine, Pathology, Infectious Diseases and Internal Medicine at the Mayo Clinic and Mayo Medical School, Rochester, MN, where a large clinical trial was conducted. Dr. Cockerill’s group compared Bactis 160US results for more than 2,800 urine specimens with results from conventional Gram stain and culture. They found that this instrument is “an effective rapid screening automated method for the detection of bacteria directly from urine samples.” Dr. Cockerill adds that “the Combact system has the potential to perform a complete urinalysis and there are plans to do pre-clinical trials both at Mayo Clinic and at the University of California/Irvine.”

To have both urinalysis and urine culture screening available on the same instrument would be an advantage for the laboratory that handles a significant number of urine specimens per year; the current cost of the instrument may preclude its usage in small and medium-sized facilities. Referring to the correct placement of this instrument, Greg Meehan, director of Marketing and Field Service for BDMS, which is involved in the clinical trials of the Bactis 160US Combact system, says, “Integration is the key to capturing the full benefit of labor savings.”

Where the instrument fits to best advantage is more important than the traditional areas of scientific discipline. This might be another situation where the “rapid response” area of the laboratory would be the most logical place for such an instrument. However, at this time, large reference laboratories are the most obvious venues for automation that requires very large volumes.

As an advancement in plate reading at the bench, MDS AutoLab offers a means of automatically linking the flow of information with the interpretative expertise of the technologist. The Microbiology Electronic Workbench System (MEWS) enables the technologist to eliminate paperwork when reading cultures; the bar coded plates are the link to work up data and culture results, in addition to patient demographic information. Scanning the plates brings up the appropriate culture information on a PC and the technologist can record follow-up work and/or finalize results here.

Stephen Middleton, director of Project Management at MDS, reports the system is customized per site and can be programmed to flag incorrect work-up of a culture according to specific facility guidelines. Because traditional paper and pencil are not used as much at the bench with MEWS and so much information is already in the system, workflow could move at a more efficient pace. Several high-volume reference laboratories are making use of this process enhancement.

Molecular Diagnostics

In the 1980s, molecular biologists’ discoveries led to the development of a biotechnology industry that continues to impact clinical microbiology. Molecular diagnostics methods are designed to detect DNA sequences that carry the unique codes for each organism and offer unprecedented sensitivity and specificity when compared with traditional laboratory identification methods.

For organisms whose culture methods are difficult or do not exist, or when a rapid answer is paramount, molecular diagnostic probe kits have been a welcome addition to the methods available in clinical microbiology. Amplification technologies have made it possible to detect a single virus or cell in a sample, which has provided the practical aspect to making headway where amount of specimen is often critical.

Although the time to final result has been appreciably shortened, some constraints exist. The assays can be fairly expensive if volume for a particular test is low, and some microbiologists feel that varying technical expertise can be a limiting factor. Gen-Probe Inc., San Diego, however, has developed a more sophisticated instrument system to completely automate nucleic acid amplification testing. Performance data is available for an HIV-1/HCV RNA assay on this platform and a more complete menu for infectious disease testing has been proposed. Again, volume and technologist time will have to be measured against overall expense to determine cost savings at each individual laboratory site.

It’s clear that the fundamental technologies for molecular diagnostics are here. What remains to be seen, however, is the integration of more automated instruments into the entire laboratory setting.

What Do Microbiologists Want?

There’s definitely a need for automation to execute the entire process that some instruments now do in a semi-automated mode. For example, the pre-analytical steps to organism identification are manual and time-consuming, which is the area that manufacturers should be concerned with to further help the laboratory. Time saved in the set-up of trays/cards for the automated system would be a welcome improvement.

Examining precision, Kevin Hazen, PhD, director of Microbiology, University of Virginia Laboratories, Charlottesville, comments, “The most frequent source of error in microbiology is derived from the initial Gram stain of a specimen.”

Does it matter if the crystal violet, iodine, etc. are timed exposures? Dr. Hazen says it might matter a great deal and his laboratory has recently acquired an automated Gram stain instrument to determine if this precise reproducibility will make a difference in correlation between initial Gram stain and culture results. Gram stain processing probably varies from technologist to technologist, but instrument-produced slides will not show this variability.

Kirk Doing, PhD, director of Clinical Microbiology and Infectious Diseases Laboratories at Affiliated Laboratories Inc. in Bangor, ME, suggests that “more rapid and readily available assays for specific resistance factors would be helpful, such as mecA gene and MRSA, Vancomycin resistant gene, etc.”

These would be desirable improvements to the semi-automated identification/susceptibility systems—it’s becoming increasingly difficult to stay abreast of emerging bacterial resistance patterns.

BDMS is responding to this challenge by developing the Phoenix Automated Identification and Susceptibility System, designed to enhance patient analysis and management.

Most microbiologists appreciate the tremendous advances in automation of blood culture systems and several requested that manufacturers take it further by developing the blood culture to probe to susceptibility pathway. To save even more time in the laboratory, the storage and retrieval of specimens and cultures should become automated. Additionally, for epidemiological purposes or other future studies, an online archival system would save time if cultures and specimens could be quickly located and automatically retrieved from a refrigerated storage unit.

It’s evident that clinical microbiologists can—and do—change as technology advances. In 1969, semi-automated blood culture instruments, automated plate streakers, bar code demographics, robotic tools, DNA/RNA amplification systems and sophisticated information systems linking the laboratory to the pharmacy, nursing station and physician were largely unknown. The challenges have changed, too. New infectious agents, re-emerging epidemiological problems and more resistant organisms have made the microbiology environment far more complex than it was 30 years ago.

Clinical microbiologists should make their needs known to automation manufacturers and developers, guiding them to improvements that would make microbiology tasks more efficient. And if patient needs are better served by the movement of some tests/assays to a rapid response area, that integration should take place.

Dianne Kelly performs diagnostic microbiology and quality assurance responsibilities at MVP Laboratories, Omaha, NE, and is an ADVANCE editorial advisory board member.

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