Perks of Molecular Microbiology

Recent advances in molecular clinical microbiology have greatly improved testing in the clinical laboratory and will continue to do so. Miniaturization of testing equipment, for instance, has reduced the amount of room needed to house it, says John G. Thomas, PhD, MS, HCLD, director, Biofilm Research Laboratory for Translational Studies and senior consultant for Clinical Microbiology, West Virginia University Hospitals, Morgantown. Dr. Thomas also is an antibiotic resistance analyst professor, Departments of Pathology and Periodontics, West Virginia University Schools of Medicine and Dentistry.

"Today's testing kits are a significant improvement compared to the days when we created our own testing kits in-house," Dr. Thomas continues. "For example, many ingredients are required for polymerase chain reaction (PCR) testing. Previously, we had to obtain all of the components from different vendors. Now we can buy testing kits as a single product to implement a test."

Additionally, several tools are now available that allow laboratories to restrict contaminants; nationally published guidelines for testing now exist; and for administrators, codes for reimbursement that address methodology have been created.

Gregory J. Tsongalis, PhD, director, Molecular Pathology and Clinical Chemistry, Dartmouth Medical School, Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, reports a rapid expansion of testing applications that could potentially result in more standardization. Additionally, more robust instruments are now available and novel platforms have been developed.

Benefits Abound

These advances in molecular clinical microbiology have benefited laboratory testing, personnel and instrumentation. One significant improvement is that turnaround times have become greatly reduced. In fact, for real-time PCR assays, results are available in as little as one hour following extraction, says Astrid K. Petrich, PhD, molecular microbiologist, Hamilton Regional Laboratory Medicine Program; and associate professor, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.

Additionally, real-time PCR assays can now be quantitative so that patients can be monitored over time, i.e., transplant patients for Cytomegalovirus (CMV), Epstein-Barr virus (EBV) and BK virus. Multiplex PCR assays with luminex detection can detect all possible pathogens causing a disease syndrome, particularly with respiratory viral disease and gastrointestinal disease.

Another benefit to testing advances is that there are less restrictive requirements for performing some tests, so they can be distributed throughout the laboratory. "Oftentimes, a microbiologist is no longer required to do certain testing, so tests can be performed on the evening or night shift," Dr. Thomas says.

"Ultimately, tests are easier and more universal and applicability in the laboratory is much more useful," he adds. "You no longer have to use a separate room to perform certain tests or have special air filters or desk and bench areas."

Personnel may have new training and growth opportunities; staff has the ability to work in other sections or bring the tests into microbiology. "As laboratory procedures become more automated, less people may be required to perform tests," Dr. Thomas notes.

Improvement in Disease Detection

Says Dr. Thomas, "Advances in molecular microbiology testing have opened up a huge avenue for laboratories that couldn't do certain tests previously due to the required expertise." At one time, standard testing methods in virology required long turnaround times for testing such as HIV, hepatitis, herpes, human papillomavirus (HPV) and respiratory viruses such influenza and Respiratory Syncytial Virus (RSV).

Slower growing bacteria, predominantly Mycobacterium tuberculosis, has also moved into the molecular identification realm, as have antibiotic resistance markers in bacteria, such as Methicillin-resistant Staphylococcus aureus (MRSA).

Multiplexing to identify most clinically significant agents for respiratory, gastrointestinal and central nervous system diseases are also headed toward the molecular identification realm.

Advances also will enable laboratory professionals to quickly and efficiently deal with routine and outbreak screening of microorganisms such as vancomycin-resistant enterococci (VRE), Clostridium difficile and Norovirus. With rapid laboratory results comes timely implementation of infection control practices, including isolation, outbreak investigation, environmental cleaning and contact tracing, Dr. Petrich adds.

Future of Disease Management

Dr. Thomas also emphasizes the importance of The Human Microbiome Project (HMP), a National Institutes of Health (NIH) initiative with the goal of identifying and characterizing the microorganisms found in association with both healthy and diseased humans. The goal of the five-year project and similar NIH-sponsored microbiome projects is to demonstrate that poorly characterized changes in the human microbiome can be associated with human health or disease.

"Now that the Human Genome Project is complete, we want to learn about genetics of the human microbes, then we will overlap the two studies," Dr. Thomas says. "This is extraordinary."

For example, when the HMP study is complete in three years, laboratorians will be able to look at the genetics of individuals at risk for cystic fibrosis (CF) and the gene of the bacterium of certain patients who have CF. They'll also be able to compare the two and see if there is a combination of human and bacterium genes that cause a patient to have CF.

"This is the future of disease management," Dr. Thomas says. "It has incredible potential for mapping diseases and the bugs that cause them. We will be able to increase the detection time and find more diseases not recognized now."

What's Next?

The microbiology laboratory will become significantly more automated in the coming years. "In the next five years, I predict that

50 percent of microbiology tests will become molecular," Dr. Thomas says. Today, that rate is less than 5 percent to 10 percent. In smaller laboratories (hospitals with less than 200 beds), very limited molecular testing is performed.

Large tertiary care and medical centers are among the first to embrace molecular microbiology because they can afford to do so, Dr. Thomas asserts. However, cost reductions will allow molecular microbiology to become more common in smaller hospital laboratories over the next five years. Fewer specialty trained technologists will be needed for testing because of the more general nature and availability of testing kits as well as concise protocols that are expected.

Dr. Thomas, a world traveler, believes that molecular testing in microbiology has been more integrated in some foreign laboratories than in the United States. "Japan's diagnostic laboratories have many more microbiology tools than those in the United States, which is very slow to adapt new methods. In the United Kingdom, I was amazed to see how much molecular integration has occurred. We can learn a lot from collaboration on a global sense," he says.

Dr. Petrich concurs. "Many hospitals have been slow to move into routine use of molecular microbiology testing due to cost issues, even though it would have a significant impact on workflow, turnaround time, sensitivity and clinical utility. Costs have come down somewhat due to competition and new technologies. Also, more studies have examined the cost effectiveness of these new tests in terms of saving the hospital money, e.g., infection control versus increased costs to the laboratories for testing. Administration is seeing the value, even though there are increased costs to the lab."

Another imminent change is that many diagnostic tests will be done from oral secretions (saliva) instead of blood. "This will make it easier for patients to undergo testing," Dr. Thomas says.

Dr. Thomas also reports a paradigm shift in microbiology. "We are in the realm where multiple organisms cause a single disease. This prompts the question: How can we detect the organisms associated with many bugs? Consider chronic wounds as an example. In microbiology, when we culture we discover two to five bugs. If we use molecular methods, we can get 18 to 25 bugs."

Additional Perks

Says Dr. Tsongalis, "We have learned a lot about the limitations and dos and don'ts of molecular testing from infectious disease applications. We will face similar issues in other complex disease molecular testing applications that are not infectious."

As assays continue to improve and become more competitive, prices are expected to decrease and technology will become more widespread in hospital laboratories. Laboratory professionals will gain skills in molecular methods, and when molecular assays are used in conjunction with existing technology, laboratory results will provide improved patient care, Dr. Petrich says.

Dr. Thomas also notes that molecular diagnostics is becoming eco-friendly. "Disposing of micro plates in an efficient manner is a significant problem," he says. "One of the byproducts of moving to molecular testing will be a reduction of waste of large pieces of plastics, pipettes, tubes and bottles of blood cultures."

One Japanese laboratory he visited has a huge array of molecular testing; its disposal is 10 percent that of a typical American lab. The amount of waste is reduced because smaller pipettes and instrumentation are used.

Ultimately, many positive changes are ahead for molecular clinical microbiology testing as advances in this field continue to occur.

Karen Appold is an editorial consultant based in Royersford, PA. Contact her at KarenAppold@comcast.net or visit her Web site at www.WriteNowServices.com.