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.
The self-cleaning material has been proven to repel even the deadliest forms of antibiotic resistant (ABR) superbugs and viruses. This ultimate non-stick coating is a chemically treated form of transparent plastic wrap which can be adhered to surfaces prone to gathering germs, such as door handles, railings, and intravenous therapy (IV) stands.
“We developed the wrap to address the major threat that is posed by multi-drug resistant bacteria,” Leyla Soleymani, PhD, Associate Professor at McMaster University and one of the leaders of the study, told CNN. “Given the limited treatment options for these bugs, it is key to reduce their spread from one person to another.”
According to research published in the peer-reviewed Southern Medical Journal, “KPC-producing bacteria are a group of emerging highly drug-resistant Gram-negative bacilli causing infections associated with significant morbidity and mortality.”
Were those surfaces covered in this new bacterial-resistant
coating, life-threatening infections in hospital ICUs could be prevented.
Taking Inspiration from Nature
In designing their new anti-microbial wrap, McMaster researchers took their inspiration from natural lotus leaves, which are effectively water-resistant and self-cleaning thanks to microscopic wrinkles that repel external molecules. Substances that come in contact with surfaces covered in the new non-stick coating—such as a water, blood, or germs—simply bounce off. They do not adhere to the material.
The “shrink-wrap” is flexible, durable, and inexpensive to
manufacture. And, the researchers hope to locate a commercial partner to
develop useful applications for their discovery.
“We’re structurally tuning that plastic,” Soleymani told SciTechDaily. “This material gives us something that can be applied to all kinds of things.”
In the video above, Leyla Soleymani, PhD, Associate Professor at McMaster University, explains how “The new plastic surface—a treated form of conventional transparent wrap—can be shrink-wrapped onto door handles, railings, IV stands, and other surfaces that can be magnets for bacteria such as MRSA and C. difficile. This may be technology that has great value to clinical laboratories and microbiology laboratories. Click here to watch the video. (Image and video copyright: McMaster University/YouTube.)
Industries Outside of Healthcare Also Would Benefit
According to the US Centers for Disease Control and Prevention (CDC), at least 2.8 million people get an antibiotic-resistant infection in the US each year. More than 35,000 people die from these infections, making it one of the biggest health challenges of our time and a threat that needs to be eradicated. This innovative plastic coating could help alleviate these types of infections.
And it’s not just for healthcare. The researchers said the coating could be beneficial to the food industry as well. The plastic surface could help curtail the accidental transfer of bacteria, such as E. coli, Salmonella, and Listeria in food preparation and packaging, according to the published study.
“We can see this technology being used in all kinds of institutional and domestic settings,” Tohid Didar, PhD, Assistant Professor at McMaster University and co-author of the study, told SciTechDaily. “As the world confronts the crisis of anti-microbial resistance, we hope it will become an important part of the anti-bacterial toolbox.”
Clinical laboratories also are tasked with preventing the
transference of dangerous bacteria to patients and lab personnel. Constant
diligence in application of cleaning protocols is key. If this new anti-bacterial
shrink wrap becomes widely available, medical laboratory managers and
microbiologists will have a new tool to fight bacterial contamination.
As infectious bacteria become even more resistant to antibiotics, chronic disease patients with weakened immune systems are in particular danger
Microbiologists
and clinical
laboratory managers in the United States may find it useful to learn that
exceptionally virulent strains of bacteria are causing increasing numbers of cancer
patient deaths in India. Given the speed with which infectious diseases spread
throughout the world, it’s not surprising that deaths due to similar hospital-acquired
infections (HAIs) are increasing in the US as well.
Recent news reporting indicates that an ever-growing number
of cancer patients in the world’s second most populous nation are struggling to
survive these infections while undergoing chemotherapy and other treatments for
their cancers.
In some ways, this situation is the result of more powerful antibiotics. Today’s modern antibiotics help physicians, pathologists, and clinical laboratories protect patients from infectious disease. However, it’s a tragic fact that those same powerful drugs are making patients with chronic diseases, such as cancer, more susceptible to death from HAIs caused by bacteria that are becoming increasingly resistant to those same antibiotics.
India is a prime example of that devastating dichotomy. Bloomberg
reported that a study conducted by Abdul
Ghafur, MD, an infectious disease physician with Apollo Hospitals in Chennai, India,
et al, concluded that “Almost two-thirds of cancer patients with a
carbapenem-resistant infection are dead within four weeks, vs. a 28-day
mortality rate of 38% in patients whose infections are curable.”
This news should serve as an alert to pathologists, microbiologists,
and clinical laboratory leaders in the US as these same superbugs—which resist
not only antibiotics but other drugs as well—may become more prevalent in this
country.
‘We Don’t Know
What to Do’
The dire challenge facing India’s cancer patients is due to escalating
bloodstream infections associated with carbapenem-resistant
enterobacteriaceae (CRE), a particularly deadly bacteria that has become
resistant to even the most potent carbapenem antibiotics, generally
considered drugs of last resort for dealing with life-threatening infections.
Lately, the problem has only escalated. “We are facing a
difficult scenario—to give chemotherapy and cure the cancer and get a
drug-resistant infection and the patient dying of infections.” Ghafur told Bloomberg.
“We don’t know what to do. The world doesn’t know what to do in this scenario.”
Ghafur added, “However wonderful the developments in the
field of oncology, they are not going to be useful, because we know cancer
patients die of infections.”
Abdul Ghafur, MD (above), an infectious disease physician with Apollo Hospitals in Chennai, India, told The Better India that, “Indians, are obsessed with antibiotics and believe that they can cure almost all infections, including viral infections! Moreover, at least half of the prescriptions by Indian doctors include an antibiotic. Sadly, the public believes that whenever we get cold and cough, we need to swallow antibiotics for three days along with paracetamol [acetaminophen]! This is a myth that urgently needs to disappear!” (Photo copyright: Longitude Prize.)
The problem in India, Bloomberg reports, is
exacerbated by contaminated food and water. “Germs acquired through ingesting
contaminated food and water become part of the normal gut microbiome, but they can
turn deadly if they escape the bowel and infect the urinary tract, blood, and
other tissues.” And chemotherapy patients, who likely have weakened digestive
tracts, suffer most when the deadly germs reach the urinary tract, blood, and surrounding
tissues.
“Ten years ago, carbapenem-resistant superbug infections
were rare. Now, infections such as carbapenem-resistant klebsiella bloodstream
infection, urinary infection, pneumonia, and surgical site infections are a
day-to-day problem in our (Indian) hospitals. Even healthy adults in the
community may carry these bacteria in their gut in Indian metropolitan cities;
up to 5% of people carry these superbugs in their intestines,” Ghafur told The
Better India.
“These patients receive chemotherapy during treatment, which
lead to severe mucositis
of gastrointestinal tract and myelosuppression.
It was hypothesized that the gut colonizer translocate into blood circulation
causing [bloodstream infection],” the AIIMS paper states.
US Cases of C. auris Also Linked to CRE
Deaths in the US involving the fungus Candida auris (C. auris)
have been linked to CRE as well. And, people who were hospitalized outside the
US may be at particular risk.
The CDC reported on
a Maryland resident who was hospitalized in Kenya with a
carbapenemase-producing infection, which was later diagnosed as C. auris. The CDC
describes C. auris as “an emerging drug-resistant yeast of high public concern
… C auris frequently co-occurs with carbapenemase-producing organisms like
CRE.”
The graphic above, developed by the NYT from CDC data, shows that Candida auris is found globally and not restricted to poor or resource-strapped nations. “The fungus seems to have emerged in several locations at once, not from a single source,” the NYT reports. This means clinical laboratories can expect to be processing more tests to identify the deadly fungus. (Graphic copyright: New York Times/CDC.)
Drug-resistant germs are a public health threat that has
grown beyond overuse of antibiotics to an “explosion of resistant fungi,”
reported the New
York Times (NYT).
“It’s an enormous problem. We depend on being able to treat
those patients with antifungals,” Matthew Fisher, PhD,
Professor of Fungal Disease Epidemiology at Imperial College London, told the NYT.
The NYT article states that “Nearly half of patients
who contract C. auris die within 90 days, according to the CDC. Yet the world’s
experts have not nailed down where it came from in the first place.”
Cases of C. auris in the US are showing up in New York, New
Jersey, and Illinois and is arriving on travelers from many countries,
including India, Pakistan, South Africa, Spain, United Kingdom, and
Venezuela.
“It is a creature from the black lagoon,” Tom Chiller, MD,
Chief of the Mycotic
Diseases Branch at the CDC told the NYT. “It bubbled up and now it
is everywhere.”
Since antibiotics are used heavily in agriculture and
farming worldwide, the numbers of antibiotic-resistant infections will likely
increase. Things may get worse, before they get better.
Pathologists, microbiologists, oncologists, and clinical
laboratories involved in caring for patients with antibiotic-resistant
infections will want to fully understand the dangers involved, not just to
patients, but to healthcare workers as well.
Technology allows retrievable information to be recorded directly into the genomes of living bacteria, but will this technology have value in clinical laboratory testing?
Researchers at Harvard Medical School have successfully used CRISPR technology to encode an image and a short film into the Deoxyribonucleic acid (DNA) of bacteria. Their goal is to develop a way to record and store retrievable information in the genomes of living bacteria. A story in the Harvard Gazette described the new technology as a sort of “biological hard drive.”
It remains to be seen how this technology might impact medical laboratories and pathology groups. Nevertheless, their accomplishment is another example of how CRISPR technology is leading to new insights and capabilities that will advance genetic medicine and genetic testing.
Recording Complex Biological Events in the Genomes of Bacteria
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are DNA sequences containing short, repetitive base sequences found in the genomes of bacteria and other micro-organisms that can facilitate the modification of genes within organisms. The term CRISPR also can refer to the whole CRISPR-Cas9 system, which can be programmed to pinpoint certain areas of genetic code and to modify DNA at exact locations.
Led by George Church, PhD, faculty member and Professor of Genetics at Harvard Medical School, the team of researchers at the Wyss Institute for Biologically Inspired Engineering at Harvard University in Cambridge, Mass., constructed a molecular recorder based on CRISPR that enables cells to obtain DNA information and produce a memory in the genome of bacteria. With it, they inserted a GIF image and a five-frame movie into the bacteria’s DNA.
“As promising as this was, we did not know what would happen when we tried to track about 100 sequences at once, or if it would work at all,” noted Seth Shipman, PhD, Postdoctoral Fellow, and one of the authors of the study in the Harvard Gazette story. “This was critical since we are aiming to use this system to record complex biological events as our ultimate goal.”
Translating Digital Information into DNA Code
The team transferred an image of a human hand and five frames of a movie of a running horse onto nucleotides to imbed data into the genomes of bacteria. This produced a code relating to the pixels of each image. CRISPR was then used to insert genetic code into the DNA of Escherichia coli (E-coli) bacteria. The researchers discovered that CRISPR did have the ability to encode complex information into living cells.
“The information is not contained in a single cell, so each individual cell may only see certain bits or pieces of the movie. So, what we had to do was reconstruct the whole movie from the different pieces,” stated Shipman in a BBC News article. “Maybe a single cell saw a few pixels from frame one and a few pixels from frame four … so we had to look at the relation of all those pieces of information in the genomes of these living cells and say, ‘Can we reconstruct the entire movie over time?’”
The team used an image of a digitized human hand because it embodies the type of intricate data they wish to use in future experiments. A movie also was used because it has a timing component, which could prove to be beneficial in understanding how a cell and its environment may change over time. The researchers chose one of the first motion pictures ever recorded—moving images of a galloping horse by Eadweard Muybridge, a British photographer and inventor from the late 19th century.
“We designed strategies that essentially translate the digital information contained in each pixel of an image or frame, as well as the frame number, into a DNA code that, with additional sequences, is incorporated into spacers. Each frame thus becomes a collection of spacers,” Shipman explained in the Harvard Gazette story. “We then provided spacer collections for consecutive frames chronologically to a population of bacteria which, using Cas1/Cas2 activity, added them to the CRISPR arrays in their genomes. And after retrieving all arrays again from the bacterial population by DNA sequencing, we finally were able to reconstruct all frames of the galloping horse movie and the order they appeared in.”
In the video above, Wyss Institute and Harvard Medical School researchers George Church, PhD, and Seth Shipman, PhD, explain how they engineered a new CRISPR system-based technology that enables the chronological recording of digital information, like that representing still and moving images, in living bacteria. Click on the image above to view the video. It is still too early to determine how this technology may be useful to pathologists and clinical laboratory scientists. (Caption and video copyright: Wyss Institute at Harvard University.)
“In this study, we show that two proteins of the CRISPR system, Cas1 and Cas2, that we have engineered into a molecular recording tool, together with new understanding of the sequence requirements for optimal spacers, enables a significantly scaled-up potential for acquiring memories and depositing them in the genome as information that can be provided by researchers from the outside, or that, in the future, could be formed from the cells natural experiences,” stated Church in the Harvard Gazette story. “Harnessed further, this approach could present a way to cue different types of living cells in their natural tissue environments into recording the formative changes they are undergoing into a synthetically created memory hotspot in their genomes.”
Encoding Information into Cells for Clinical Laboratory Testing and Therapy
The team plans to focus on creating molecular recording devices for other cell types and on enhancing their current CRISPR recorder to memorize biological information.
“One day, we may be able to follow all the developmental decisions that a differentiating neuron is taking from an early stem cell to a highly-specialized type of cell in the brain, leading to a better understanding of how basic biological and developmental processes are choreographed,” stated Shipman in the Harvard Gazette story. Ultimately, the approach could lead to better methods for generating cells for regenerative therapy, disease modeling, drug testing, and clinical laboratory testing.
According to Shipman in the BBC News article, these cells could “encode information about what’s going on in the cell and what’s going on in the cell environment by writing that information into their own genome.”
This field of research is still new and its full potential is not yet understood. However, if this capability can be developed, there could be opportunities for pathologists and molecular chemists to develop methods for in vivo monitoring of a patient’s cell function. These methods could prove to be an unexpected new way for clinical laboratories to add value and become more engaged with the clinical care team.
New vaccine has potential to reduce volume of clinical laboratory testing for bacterial and viral infections
By now, nearly all pathologists and clinical laboratory scientists acknowledge that advances in molecular diagnostics and genetic testing are contributing to significant improvements in patient care. Now comes news of a comparable breakthrough in another field of medicine with the potential to protect many individuals from pneumonia and similar infectious diseases.
A new way to develop vaccines made the news recently. Researchers at the University of Buffalo (UB) in New York have found a new way to reduce infections of specific and widespread Streptococcus pneumoniae (pneumococcus) diseases.
This cutting-edge pneumococcal vaccine allows Streptococcus pneumoniae to colonize and live inside the body as long as there is no risk to the host. When a threat is detected, the vaccine establishes an immune system response to annihilate the disease-causing bacteria. (more…)
