New technology could enable genetic scientists to identify antibiotic resistant genes and help physicians choose better treatments for genetic diseases
Genomic scientists at the Icahn School of Medicine at Mount Sinai Medical Center in New York City have developed what they call a “smart tweezer” that enables researchers to isolate a single bacterium from a patient’s microbiome in preparation for genetic sequencing. Though primarily intended for research purposes, the new technology could someday be used by clinical laboratories and microbiologists to help physicians diagnose chronic disease and choose appropriate genetic therapies.
The researchers designed their new technology—called mEnrich-seq—to improve the effectiveness of research into the complex communities of microorganisms that reside in the microbiomes within the human body. The discovery “ushers in a new era of precision in microbiome research,” according to a Mount Sinai Hospital press release.
“Imagine you’re a scientist who needs to study one particular type of bacteria in a complex environment. It’s like trying to find a needle in a large haystack,” said the study’s senior author Gang Fang, PhD (above), Professor of Genetics and Genomic Sciences at Icahn School of Medicine at Mount Sinai Medical Center, in a press release. “mEnrich-seq essentially gives researchers a ‘smart tweezer’ to pick up the needle they’re interested in,” he added. Might smart tweezers one day be used to help physicians and clinical laboratories diagnose and treat genetic diseases? (Photo copyright: Icahn School of Medicine.)
Addressing a Technology Gap in Genetic Research
Any imbalance or decrease in the variety of the body’s microorganisms can lead to an increased risk of illness and disease.
In researching the microbiome, many scientists “focus on studying specific types of bacteria within a sample, rather than looking at each type of bacteria present,” the press release states. The limitation of this method is that a specific bacterium is just one part of a complicated environment that includes other bacteria, viruses, fungi and host cells, each with their own unique DNA.
“mEnrich-seq effectively distinguishes bacteria of interest from the vast background by exploiting the ‘secret codes’ written on bacterial DNA that bacteria use naturally to differentiate among each other as part of their native immune systems,” the press release notes. “This new strategy addresses a critical technology gap, as previously researchers would need to isolate specific bacterial strains from a given sample using culture media that selectively grow the specific bacterium—a time-consuming process that works for some bacteria, but not others. mEnrich-seq, in contrast, can directly recover the genome(s) of bacteria of interest from the microbiome sample without culturing.”
Isolating Hard to Culture Bacteria
To conduct their study, the Icahn researchers used mEnrich-seq to analyze urine samples taken from three patients with urinary tract infections (UTIs) to reconstruct Escherichia coli (E. Coli) genomes. They discovered their “smart tweezer” covered more than 99.97% of the genomes across all samples. This facilitated a comprehensive examination of antibiotic-resistant genes in each genome. They found mEnrich-seq had better sensitivity than standard study methods of the urine microbiome.
They also used mEnrich-seq to selectively examine the genomes of Akkermansia muciniphila (A. muciniphila), a bacterium that colonizes the intestinal tract and has been shown to have benefits for obesity and Type 2 diabetes as well as a response to cancer immunotherapies.
“Akkermansia is very hard to culture,” Fang told GenomeWeb. “It would take weeks for you to culture it, and you need special equipment, special expertise. It’s very tedious.”
mEnrich-seq was able to quickly segregate it from more than 99.7% of A. muciniphila genomes in the samples.
Combatting Antibiotic Resistance Worldwide
According to the press release, mEnrich-seq could potentially be beneficial to future microbiome research due to:
Cost-Effectiveness: It offers a more economical approach to microbiome research, particularly beneficial in large-scale studies where resources may be limited.
Broad Applicability: The method can focus on a wide range of bacteria, making it a versatile tool for both research and clinical applications.
Medical Breakthroughs: By enabling more targeted research, mEnrich-seq could accelerate the development of new diagnostic tools and treatments.
“One of the most exciting aspects of mEnrich-seq is its potential to uncover previously missed details, like antibiotic resistance genes that traditional sequencing methods couldn’t detect due to a lack of sensitivity,” Fang said in the news release. “This could be a significant step forward in combating the global issue of antibiotic resistance.”
More research and clinical trials are needed before mEnrich-seq can be used in the medical field. The Icahn researchers plan to refine their novel genetic tool to improve its efficiency and broaden its range of applications. They also intend to collaborate with physicians and other healthcare professionals to validate how it could be used in clinical environments.
Should all this come to pass, hospital infection control teams, clinical laboratories, and microbiology labs would welcome a technology that would improve their ability to detect details—such as antibiotic resistant genes—that enable a faster and more accurate diagnosis of a patient’s infection. In turn, that could contribute to better patient outcomes.
It can take up to eight days after onset of symptoms for a person’s immune system to develop antibodies, so serological tests are not designed for diagnosing recent or active infections, stated a Mayo Clinic news story. However, Reuters reported that the availability of serological tests is “a potential game changer” because they could identify people who are immune even if they had no symptoms or only mild symptoms.
“Ultimately, this might help us figure out who can get the country back to normal,” Florian Krammer, PhD, told Reuters. Krammer’s lab at the Icahn School of Medicine at Mount Sinai in New York City has developed a serological test. “People who are immune could be the first people to go back to normal life and start everything up again,” he said.
However, some experts advise that the presence of antibodies is not necessarily a “get out of jail free” card when it comes to the coronavirus. “Infectious disease experts say immunity against COVID-19 may last for several months and perhaps a year or more based on their studies of other coronaviruses, including Severe Acute Respiratory Syndrome (SARS), which emerged in 2003,” reported Reuters. “But [the experts] caution that there is no way to know precisely how long immunity would last with COVID-19, and it may vary person to person.”
Additionally, it is also “uncertain whether antibodies would be sufficient protection if a person were to be re-exposed to the virus in very large amounts,” such as in an emergency room or ICU, Reuters reported.
Serological Survey Studies Get Underway Worldwide
Aside from detecting potential immunity, the World Health Organization (WHO) says serological tests could be useful for widespread disease surveillance and epidemiological research.
In the US, the Vitalant
Research Institute is leading several large serological survey or
“serosurvey” studies in which regional blood centers save samples of donated
blood for antibody testing, Science
reported.
Science also reported on a similar WHO initiative in which six countries will pool data from their own antibody studies. And in the Netherlands, blood banks have begun screening thousands of blood donations for presence of antibodies, Wired reported.
FDA Emergency Use Authorization
On March 16, the federal Food and Drug Administration (FDA) announced that it would allow commercial development and distribution of serological tests that “identify antibodies (e.g., IgM, IgG) to SARS-CoV-2 from clinical specimens” without an Emergency Use Authorization (EUA). The agency noted that these tests are “less complex than molecular tests” used to detect active infections, and that the policy change is limited to such testing in medical laboratories or by healthcare workers at the point-of-care. “This policy does not apply to at home testing,” the FDA reiterated.
“Serological tests can play a critical role in the fight against COVID-19 by helping healthcare professionals to identify individuals who have overcome an infection in the past and have developed an immune response,” said FDA Commissioner Stephen M. Hahn, MD (above with President Trump during a Coronavirus Task Force press briefing), in an April 7 press statement. “In the future, this may potentially be used to help determine—together with other clinical data—that such individuals are no longer susceptible to infection and can return to work. In addition, these test results can aid in determining who may donate a part of their blood called convalescent plasma, which may serve as a possible treatment for those who are seriously ill from COVID-19.” (Photo copyright: CNBC.)
FDA Issues First EUA for Rapid Diagnostic Test
Cellex Inc., based in Research Triangle Park, N.C., received the first EUA for its qSARS-CoV-2 serological test on April 1. As with other rapid diagnostic tests (RDTs) under development, the qSARS-CoV-2 test detects the presence of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies in human blood. The biotechnology company’s RDT can be used to test serum, plasma, or whole-blood specimens, stated Cellex, and can produce results in 15 to 20 minutes.
The FDA has authorized use of the antibody test only by laboratories certified under CLIA to perform moderate and high complexity tests. Cellex has set up a COVID-19 website with information about the qSARS-CoV-2 test for clinical laboratories, patients, and healthcare providers.
Other Serological Tests Under Development
Mayo
Clinic Laboratories announced on April 13 that it is ramping up
availability of an internally-developed serological test. “Initial capacity
will be 8,000 tests per day performed at laboratory locations across Mayo Clinic,” stated the announcement.
“Testing will be performed 24 hours a day, and Mayo Clinic Laboratories is working
to ensure turnaround time is as close as possible to 24 hours after receipt of
the sample.”
Emory University in Atlanta announced on April 13 that it will begin deploying its own internally developed antibody test. Initially, testing will be limited to 300 people per day, comprised of Emory Healthcare patients, providers, and staff members. Eventually, testing will be “expanded significantly,” said Emory, with a goal of 5,000 tests per day by mid-June.
RDTs are typically qualitative, meaning they produce a
positive or negative result, stated the Center for Health Security. An ELISA
test “can be qualitative or quantitative,” noted the Center, but it can take
one to five hours to produce results.
A third type of serological test—the neutralization assay—involves infecting a patient’s blood with live coronavirus to determine if antibodies exist that can inhibit growth of the virus. The test takes three to five days in a level 3 biosafety laboratory to produce results. The Straits Times reported on one laboratory in Singapore that developed a neutralization assay to trace the source of COVID-19 infections that originated in Wuhan, China.
Serological testing is another important tool clinical
laboratories and epidemiologists can use to fight and ultimately defeat the
COVID-19 pandemic and is worth watching.
Clinical laboratories and pathology groups may eventually use these devices to detect minute quantities of biomarkers
IBM has regularly declared its interest in being a player in the field of healthcare big data. Now comes news that the information technology giant wants to develop lab-on-a-chip (LOC) technology that can handle different types of clinical laboratory and anatomic pathology tests.
As reported in Nature Nanotechnology, researchers at IBM are working with a team from Mount Sinai Health System. Together, they created a lab-on-a-chip device capable of separating biomolecules as small as 20nm in length from urine, saliva, or blood samples without the need for specialized clinical laboratory equipment. The technology is called nanoDLD.
Current testing of this lab-on-a-chip focuses on exosomes and cancer research. However, researchers note that the asymmetric pillar array on their silicon chip can also separate DNA, viruses, and protein complexes. With further development, they hope to separate particles down to 10nm in length. This would allow isolation of specific proteins. (more…)
Many of these new technologies could help pathologists develop new diagnostic tests and offer medical laboratories opportunities to expand their services
This is a competition and each year The Scientist has a panel of five experts in life sciences review the entries. Among this year’s Top Ten Innovations are promising diagnostic tools and new technologies with the potential to disrupt the current state of healthcare. In the near future, most of these technologies will be used by researchers to better understand the underlying, genetic cause of diseases and advance new treatments. However, some of these innovative technologies have already been adopted for clinical use. Others are probably several years away from becoming the basis for new medical laboratory tests.
Here is a short overview of The Scientist magazine’s list of “Top Ten Innovations for 2014.” (more…)
