Post-Genomic Microbiology


Sequencing the human genome changed the laboratory world. Today, Culture-OMICs and rapid transition pose to change it again

Vol. 24 • Issue 11 • Page 12
Cover Story

The sequencing of the human genome was the shot heard ’round the laboratory world. And while every healthcare discipline has evolved in the face of rapid-fire technological change, nowhere has this blast away from the past been more fierce and redefining than in microbiology labs.

“Microbiology is not in a state of evolution; it is in a state of revolution,” said University of West Virginia Prof. Emeritus John Thomas, PhD, director, microbiology core laboratory, Allegheny Health Network, Pittsburgh. The daily ammunition – molecular testing – is rewriting the disease-fighting battlefield parameters of microbiology, once squarely rooted in Louis Pasteur’s “one bug, one disease” mentality. This new “OMICs” age confers upon micro a more expansive knowledge of the complexity of mixed-infection diseases, the personalization of diseases and the ability to more rapidly detect diseases or symptoms.

“Having completely sequenced the genomes of many microorganisms, we now have information allowing newer and more specific tests to be developed on new technologies revolutionizing the field of microbiology,” concurred Sherry Dunbar, PhD, senior director, global scientific affairs, Luminex Corp., Austin, Texas.

David Martin, MD, CEO of AvidBiotics, also noted that the technologies developed out of the Human Genome Project have enabled the identification and ­characterizations of the many health microorganisms (microbiota) in and on our bodies.

“We are beginning to understand their relationships with each other and our own cells, and the multitude of roles and responsibilities they have in normal human development and maintenance of health. By far the majority of these microbes cannot be cultured in the laboratory. Without molecular technology, we would still have little appreciation of the importance of microbiota and the importance of protecting them from broad spectrum antibiotics,” Martin said.

Culture-OMICs Begin

Long-held truths have been rewritten somewhat within the molecular age. “We are no longer tied to ‘one bug, one disease,'” said Thomas. “We have shifted with our understanding that many diseases are chronic, complex and comprised of mixed organisms. Many of the organisms that we now know cause disease are very difficult to grow in a culture dish; we can’t always wait. We have had to readjust what we do in the lab to get results out much faster.”

Thomas joked that “there has been a traditional love/hate relationship between microbiologists and chemists – chemistry being more a technical science and microbiology being somewhat a scientific art form. It’s funny, because microbiology has now turned to a classic chemistry instrument – mass spectrometry – which defines the weight of either protein or DNA in a very short time – 5 to 10 minutes.”

Thomas believes microbiology is in the midst of a two-phased transition giving rise to what he has dubbed “Culture-OMICs.” “The tools available now, including mass spec, still depend upon culture growth,” he explained. You use a plate and a viable organism, then ionize it with a laser and measure its fractional parts, defining the microbe by migration of the DNA/protein in a vacuum in a very short time frame. If you look at the cost of the individual test (independent of the cost of the instrumentation), it’s down to about 10 cents per test – very inexpensive. That’s where we will see some downstream savings.”

The other parallel which is changing microbiology is the “OMICs” part of the term, “allowing the detection of DNA or RNA through polymerase chain reaction (PCR). Those two together will complement each other,” he noted.

Thomas said MALDI TOF mass spec will be devoted to more traditional purposes (e.g., testing stool samples). “But PCR will be applied to those things we formerly couldn’t do quickly enough – spinal fluids, blood and viruses – which many educated minds see as the future of the microbiology laboratory,” he noted, as will be animal microbes (zoonosis). “The viral diseases, for which we have never been driven – because there’s been basically no treatment as there is with bacteria, which PCR can identify – are worldwide and are still the most prevalent infectious diseases. And as we move into the future, PCR and the OMICs part of this Culture-OMICs pairing will become a larger player in their detection.”

Tests, Platforms and Microscopes

As technology moves forward, development of new assays races to keep time. “Real-time PCR has become routine, mass spectrometry is now replacing older biochemical test methods,” concurred Dunbar. “NGS is being applied heavily to studying the microbiome and a lot of the new information about our normal flora is being directly applied in practice – stool transplantation for Clostridium difficile-associated colitis comes to mind.” She also noted that syndromic panels that target multiple etiologies for particular disease states have also become an efficient way to perform diagnostic testing.

Thomas added, “Things like Biofire, Inverigin – the two systems on the market now that have been driven by Ebola – are going to be larger players in selected cases – blood, CSF, outbreaks. MALDI TOF will remain the workhorse for the next 15 years. But it is a Band-Aid, taking us from Louis Pasteur to the next generation of systems out there. And they are rapidly coming.”

That said, Thomas also pointed out there is an element to testing that will not change. “If we get a crummy specimen, we will still get a crummy result. Microbiology, more than any of the other clinical sciences, is still dependent on quality of the specimen. No matter how sophisticated the instrument, ‘Junk in, junk out’ still applies.”

For that reason alone, the microscope is not likely to disappear from lab benches. “A microscope is still the best evaluation of the quality of the specimen and the presence of cells. Today that is done by humans. In the future? At some point a computer will be able to pick up fine differences that the human eye cannot. Microscopes will stay, but who will read them remains to be seen down the road,” said Thomas.

Dunbar, however, sees a secure future for this early bit of technology in the theater of human intelligence. “Microscopes will never be obsolete to a true microbiologist. Sometimes we just want or need to see things for ourselves,” she said. “In addition, there will still be some manual tests and the need for traditional microbiology, especially for rarer organisms that do not occur frequently. These are likely not available on newer platforms, yet they are just as important and still need a pathway to an accurate diagnosis.”

Staffing Changes

Technology will have an effect on micro lab staffing in various ways, most assuredly by allowing staff contraction. “This kind of revolution will require less hands-on time because technology implementation will include the acquisitions of laboratory robotics,” detailed Thomas. “Manual labor for repetitive tasks that do not require intelligence will not be done by people; it will be done by instruments. For example, the entire set-up – from labeling tubes to streaking them to putting plates that have been streaked onto a conveyor belt and into an incubator – is automated. Preanalytic specimen preparation will all be robotic. And robots will also carry specimens from place to place – taking over the transport function of a courier or lab person. They will free up human intelligence for other tasks.”

However, not as many (human) staff members will be required in micro labs of the future. “I see a 15-20 percent reduction in lab staffs coming in the next 5 years in labs who go to automation,” said Thomas. “I’ve been told by labs that have already gone this route that, thanks to attrition, an aging workforce ready to retire and even prior staff shortages, there has been no screaming related to layoffs.”

Thomas also believes that the laboratorian of the future will be a different sort of personality, given the shifts in the work. “Microbiologists of the past have always had a loop and a plate. The microbiologists of the future will likely be computer geeks and biochemists as we transition from ‘art form’ to technology,” said Thomas.

Dunbar said some re-education will be necessary. “The great news is now that more technology platforms are configured to provide automated documentation and reduce or eliminate the amount of paperwork, it will allow time to focus on new activities, such as expanding the test menu.”

Martin also pointed out that new capabilities pegged to recognizing microbiota will require an expanded skill set. “The growing recognition of the intimate relationships between our microbiota and essentially each of our organ and physiologic systems demands that we begin formally to retrain and re-educate physicians, physiologists and other healthcare professionals in the pertinent microbiology, and microbiologists themselves in organ and systems biology/physiology,” he declared.

Holistic Health

The continued exploration of microbiota will indeed bring microbiologists into closer collaboration with care providers. New-age microbiology will likely become a key player in holistic health systems, as deeper understanding of microbes paints pictures of individual “health status,” a phrase coined by Thomas, and will inform and guide treatment ­throughout all levels of healthcare.

“We now clearly understand that we and our microbes have to ‘get along’ to be healthy,” Thomas explained. “They provide a significant part of our capability to deal with stress – both in terms of infectious diseases and otherwise. We now understand that the interaction between bugs in the gut and the brain may be more significant than we ever realized.”

Microbiology will continue to refine and define the signature of what is normal in the host individual, and what their personal health status is. “With this potent combination of Culture-OMICs, we can determine every bug that is present in a sample, and get an impression – a signature – of the microbial pool of a person. That pool has predictive value on health and disease – both good things and bad things,” detailed Thomas. “That will be a whole value-added part of the microbiology report which we have never before had the capability of doing. In addition to defining a pathogen, we will also define the overall organism pool and will learn a patient’s ability to fight that pathogen based on his inflammatory response, his bug pools, microbes he doesn’t have and ­probiotics that might be the best treatment. Microbial flora has the potential to tell us about a patient’s ability to live longer, to avoid diabetes, to circumvent obesity. It is powerful.”

Future of Microbiology

The microbiology revolution has been on the march for some time. British microbiologists Mark J. Pallen, Nicholas J. Loman and Charles W. Penn, writing in Current Opinion in Microbiology (13(5):625-631), foretold the future this way:

“The most revolutionary effect of this ‘disruptive technology’ is likely to be creation of a novel sequence-based, culture-independent diagnostic microbiology that incorporates microbial community profiling, metagenomics and single-cell genomics. We should prepare for the coming ‘technological singularity’ in sequencing, when this technology becomes so fast and so cheap that it threatens to out-compete existing diagnostic and typing methods in microbiology.”

It would seem their prediction is coming to pass. But Thomas believes one remaining question is perhaps the most important one of all: Will there be benefit to the patient?

“In the past, microbiologists have been hammered for holding results as they waited for specimens to grow. Well that’s changing,” said Thomas. “We are moving toward the concept of a 24-hour micro lab where we get the results out within an hour. The question is: What happens if those results are auto-released at 3 a.m.? Will there be anyone there to make a decision to change, alter or pull off antibiotics? The expanded micro lab will impact the workload of the physicians on the other end. How they handle that is going to be interesting. In my mind, that’s the 24 thousand dollar question. The new micro lab can only make a difference in outcomes if the medical staff stands ready to respond.”


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Valerie Neff Newitt
Valerie Neff Newitt

Staff Writer

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