Category: Biotech

DNA sequence signal for the activation of human genes. Each tiny human cell contains about six feet of DNA, a double-helical molecular chain containing four types of several billion chemical nucleotides — adenine (A), cytosine (C), guanine (G) and thymine (T) — arranged in a specific sequence, or code, that when transcribed guide the cell into producing specific proteins. (credit: University of California — San Diego)

Molecular biologists at the University of California, San Diego (UC San Diego) have discovered a short sequence of DNA that is essential for turning on (expressing proteins) more than half of all human genes — an achievement that should provide scientists with a better understanding of how human genes are regulated.

Knowing what turns on genes is important. Each human cell contains about six feet of DNA, a double-helical molecular chain containing several billion chemical nucleotides — adenine (A), cytosine (C), guanine (G) and thymine (T) — arranged in a specific sequence, or code. Active genes undergo a process called transcription, in which the nucleotide sequence in DNA is read and converted into a sister language called RNA for processing. The processed RNA sequence then guides the cell to produce specific proteins that are essential for normal cellular functions.

A depiction of the double helical structure of DNA. Its four nucleotide coding units (A, T, C, G) are color-coded in pink, orange, purple and yellow. (credit: NHGRI)

“In these six feet of DNA, there are tens of thousands of genes, which are segments of DNA that direct specific functions, such as the production of a hormone or an enzyme,” explains James T. Kadonaga, PhD, a molecular biology professor at UC San Diego who headed the team of researchers. “It is essential for the cell to control the activity of each of its tens of thousands of genes, because the improper control of gene activity can lead to adverse outcomes such as cell death or the formation of a cancer cell.”

The “human Initiator”

Enter the “Initiator.” The initiation of gene expression often occurs at a critical DNA sequence code called the “human Initiator.” This small piece of DNA helps gene expression machinery locate exactly where to begin transcribing. Although the concept of the Initiator has been known since the 1980s, the precise DNA sequence comprising the Initiator had eluded scientists.*

“There are many sequence signals that control gene activity in human cells and the Initiator is the most commonly occurring sequence at the start sites of genes,” Kadonaga said. Kadonaga and his team employed emerging genomic techniques and devised novel computational strategies to unlock the exact DNA sequence code for the human Initiator.

They also discovered that this sequence is located precisely at the start site of more than half of all human genes, underlining the importance of the human Initiator in the human genome. “The solution of the human Initiator code will enable us to explore new frontiers in gene regulation,” said Kadonaga. “In the future, it will be possible to use the code to identify other regulatory signals and in this way gain a more complete understanding of how human genes are turned on and off.”

“The authors verified the Initiator sequence in multiple cell lines, which is an impressive finding,” a scientist not involved in the studies told KurzweilAI. “However, none of these cell lines reflect normal human biology — they are essentially cancer cells proliferating in a dish. I would have liked to see this Initiator sequence verified in normal human cells from healthy patients.”

The research, now online and to be detailed in the February 10 print issue of the journal Genes & Development, was supported by grants from the National Institutes of Health.

* First observed by Pierre Chambon and his colleagues in Strasbourg, France in 1980, the human Initiator and its role in gene activation were articulated in 1989 by two MIT biologists, Stephen Smale and David Baltimore at MIT, who later revealed the approximate sequence code of the Initiator. Since then, however, other scientists had proposed a number of different sequences for the human Initiator, but none of them were found to be consistently associated with the start sites of human genes. As a result, the true Initiator sequence code remained a mystery — until now.

Abstract of The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters

DNA sequence signals in the core promoter, such as the initiator (Inr), direct transcription initiation by RNA polymerase II. Here we show that the human Inr has the consensus of BBCA₊₁BW at focused promoters in which transcription initiates at a single site or a narrow cluster of sites. The analysis of 7678 focused transcription start sites revealed 40% with a perfect match to the Inr and 16% with a single mismatch outside of the CA₊₁ core. TATA-like sequences are underrepresented in Inr promoters. This consensus is a key component of the DNA sequence rules that specify transcription initiation in humans.

Carbapenem-resistant Enterobacteriaceae (CRE) bacteria (credit: Melissa Brower/CDC)

The death of a hospitalized patient in Reno Nevada for whom no available antibiotics worked highlights what World Health Organization and other public-health experts have been warning: antibiotic resistance is a serious threat and has gone global.

The patient — a female in her 70s — was admitted in for an infection and died in September 2016 from septic shock the CDC announced on Jan. 13. The patient had been treated for multiple infections in India before traveling to the United States. The infection that led to her hospitalization in Reno was caused by a strain of carbapenem-resistant Enterobacteriaceae (CRE)* bacteria known as Klebsiella pneumoniae. Although not all strains of Klebsiella pneumonia are CRE, the strain that infected this patient was resistant to all available antibiotics, according to the CDC. (Carbapeneum is a “drug of last resort.”)

In a paper in The Lancet in October, researchers reported that more than a third of blood infections in newborn babies involving Klebsiella pneumoniae and similar bacteria were resistant to multiple drugs to the point they were virtually untreatable and “threaten the return of a pre-antibiotic era in Indian neonatal intensive care units,” the study’s authors warned.

Spreading more widely and stealthily that thought

Highlighting the importance of this report, a new NIH-funded study published online January 16, 2017 in PNAS (Proceedings of the National Academy of Sciences) from Harvard T.H. Chan School of Public Health and the Broad Institute of MIT and Harvard found that the CRE family of highly drug-resistant and potentially deadly bacteria may be spreading more widely — and more stealthily — than previously thought.

The researchers examined CRE bacteria that were isolated from patients with infections at four U.S. hospitals. They found a wide variety of CRE . They also found a diverse array of genetic traits enabling CRE to resist antibiotics, and found that these traits are transferring easily among various CRE species.

The findings suggest that CRE may well be transmitting from person to person asymptomatically, and that genomic surveillance of this dangerous bacteria should be increased.

CRE are a class of bacteria that is resistant to multiple antibiotics, including carbapenems, which are considered last-resort drugs when other antibiotics have failed. CRE, which tend to spread in hospitals and long-term care facilities, cause an estimated 9,300 infections and 600 deaths in the U.S. each year, according to the CDC — and incidence is on the rise. CDC director Tom Frieden has called these “nightmare bacteria” because they are resistant to some of the last-ditch treatments available to doctors battling resistant infections.

A type of ultraviolet light called UVC could aid hospitals in the ongoing battle to keep drug-resistant bacteria from lingering in patient rooms and causing new infections. A CDC-NIH-funded study led by Duke Health and published in The Lancet finds use of UVC machines can cut transmission of four major superbugs by a cumulative 30 percent. (credit: Shawn Rocco/Duke Health)

Unobserved transmissions

“While the typical focus has been on treating sick patients with CRE-related infections, our new findings suggest that CRE is spreading beyond the obvious cases of disease,” said William Hanage, associate professor of epidemiology at Harvard Chan School and senior author of the study. “We need to look harder for this unobserved transmission within our communities and healthcare facilities if we want to stamp it out.”

The researchers looked at about 250 samples of CRE from hospitalized patients from three Boston-area hospitals and from one California hospital.

The researchers found what Hanage termed a “riot of diversity,” both among CRE species and among carbapenem resistance genes. They also found that resistance genes are moving easily from species to species, contributing to a continually evolving threat from CRE.

In addition, the researchers found that some CRE bacteria employ uncharacterized resistance mechanisms—implying that there are more to be discovered. The finding highlights the need for vigilance in searching for as yet unknown forms of resistance as they evolve and emerge.

What if there were no new antibacterial drugs?

But what’s also needed is new antibiotics. “Meaningful incentives for pharmaceutical companies have been suggested to encourage them to re-enter this area of drug development; these incentives include models to push companies to develop these drugs or by making it economically viable so as to pull companies back to this area as well as alternative routes of funding,” notes Prof Laura J V Piddock, Antimicrobial Agents Research Group, School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham in “The crisis of no new antibiotics—what is the way forward?” in Lancet Infect Dis. in 2012.

“Also, few data exist on the human and economic costs of antibacterial resistance or the potential costs of inaction (i.e., what would the social effects be if no new antibacterial drugs were available and fatal infections became the norm?). To assess such costs, involvement of governmental agencies that recommend use of drugs is needed (i.e., FDA, European Medicines Agency, and in individual countries such as UK, The National Institute for Health and Clinical Excellence).”

* “Carbapenems are one of few antimicrobials that have been effective against multidrug-resistant bacteria, but their utility is threatened by the emergence of carbapenem-resistant Enterobacteriaceae (CRE),” according to an open-access PLoS ONE paper published in 2014. “Klebsiella pneumoniae is the most common CRE species in the United States, typically encountered as a hospital-acquired infection with high morbidity and mortality, and resistant to nearly all available antibiotics.” In this case, metallo-β-lactamase NDM-1 (New Delhi metallo-beta-lactamase or NDM), a version of Klebsiella pneumoniae, was found.

A synthetic cardiac stem cell (left) mirroring a real cardiac stem cell (right), offering therapeutic benefits without the associated risks (credit: Alice Harvey/NC State University)

Scientists have created the first synthetic version of a cardiac stem cell, offering therapeutic benefits comparable to those from natural stem cells — but without the risks and limitations, according to researchers from North Carolina State University, the University of North Carolina at Chapel Hill, and First Affiliated Hospital of Zhengzhou University in China.

The newly created “synthetic stem cells” (not actual stem cells — not even cells — just clever mimics) cannot replicate. That means they could reduce some of the risks associated with natural stem-cell therapies — including tumor growth and immune rejection. The synthetic stem calls would also avoid the fragility of natural stem cells, which require careful storage and a multi-step process of typing and characterization before they can be used.

Simulating cardiac stem cells with synthetic stem cells: a cargo-shell strategy

In an in vitro (test tube) experiment described in an open-access paper in Nature Communications, the scientists created synthetic “cell-mimicking microparticles” (CMMPs) and tested them on a mouse model with myocardial infarction.

The scientists found that the CMMPs’ ability to bind to cardiac tissue and promote growth after a heart attack was comparable to that of cardiac stem cells. But unlike cardiac (and other) natural stem cells, the synthetic stem cells have better preservation stability, and the technology is also generalizable to other types of stem cells, according to the researchers.

A cargo-and-shell strategy. The therapeutic potential of CMMPs was successfully tested in tissue repair of a mouse model of myocardial infarction. To create the synthetic stem cell, a microparticle (MP) was first fabricated from PLGA, or poly(lactic-co-glycolic acid) — a biodegradable, biocompatible polymer that serves as a dissolvable carrier. The MP contained conditioned media and growth factors* (the “cargo”) from cardiac stem cells (CSC) in its polymeric core — forming a synthetic cell-mimicking microparticle (CMMP). To prevent an immune reaction, the researchers also cloaked the CMMP with a coating from the cardiac stem-cell membrane (forming the “shell”). (credit: Junnan Tang et al./Nature Communications)

“The synthetic cells operate much the same way a deactivated vaccine works,” explains research-team leader Ke Cheng, associate professor of molecular biomedical sciences at NC State, associate professor in the joint biomedical engineering program at NC State and UNC, and adjunct associate professor at the UNC Eshelman School of Pharmacy. “[The synthetic cells'] membranes allow them to bypass the immune response, bind to cardiac tissue, release the growth factors, and generate repair, but they cannot amplify [and thus risk out-of-control growth, leading to tumors] by themselves. So you get the benefits of stem cell therapy without risks.”

Multiple stem-cell types and organs

The synthetic stem cells are also much more durable than human stem cells, they can tolerate harsh freezing and thawing, and they don’t have to be derived from the patient’s own cells, the researchers note.

“Although our first application targeted the heart, the CMMP strategy represents a platform technology that can be applied to multiple stem cell types and the repair of various organ systems,” the authors state in the paper.

The work was funded in part by the National Institutes of Health, NC State Chancellor’s Innovation Fund, and University of North Carolina General Assembly Research Opportunities Initiative grant.

* Stem-cell therapies work by secreting “paracrine factors,” including proteins and genetic materials, that aid damaged tissue in repairing itself.

Abstract of Therapeutic microparticles functionalized with biomimetic cardiac stem cell membranes and secretome

Stem cell therapy represents a promising strategy in regenerative medicine. However, cells need to be carefully preserved and processed before usage. In addition, cell transplantation carries immunogenicity and/or tumorigenicity risks. Mounting lines of evidences indicate that stem cells exert their beneficial effects mainly through secretion (of regenerative factors) and membrane-based cell-cell interaction with the injured cells. Herein, we fabricated a synthetic cell-mimicking microparticle (CMMP) that recapitulates stem cell functions in tissue repair. CMMPs carries similar secreted proteins and membranes as genuine cardiac stem cells do. In a mouse model of myocardial infarction, injection of CMMPs leads to preservation of viable myocardium and augmentation of cardiac functions similar to cardiac stem cell therapy. CMMPs (derived from human cells) do not stimulate T cells infiltration in immuno-competent mice. In conclusion, CMMPs act as “synthetic stem cells” which mimic the paracrine and biointerfacing activities of natural stem cells in therapeutic cardiac regeneration.

This cartoon depicts turning back the aging clock through cellular regeneration of progeria mice (credit: Juan Carlos Izpisua Belmonte Lab/Salk Institute)

Salk Institute scientists have extended the average lifespan of live mice by 30 percent, according to a study published December 15 in Cell. They did that by rolling back the “aging clock” to younger years, using cellular reprogramming.

The finding suggests that aging is reversible by winding back an animal’s biological clock to a more youthful state and that lifespan can be extended. While the research does not yet apply directly to humans, it promises to lead to improved understanding of human aging and the possibility of rejuvenating human tissues.

To achieve this, the scientists worked with “progeria” mouse models — mice that had been genetically modified to carry a mutation that leads to premature aging (allowing the aging effects to be isolated and studied).*

Rather than attempting to correct the genetic mutations that cause premature aging (a difficult challenge), the Salk team instead focused on restoring the epigenome (a system of chemical marks on the genome that control which genes are or are not expressed as proteins)**.

Partial reprogramming avoids tumors and aging effects

To wind back the clock, the scientists first reprogrammed progeria mouse adult cells (such as skin cells) into an induced pluripotent stem (iPS) cells*** — an early embryonic state in which the cell is not yet specialized (“differentiated”) and can be programmed to perform specific functions, such as becoming part of the skin or heart.

To generate iPS cells, fibroblasts (or another type of adult somatic cell) are transduced with retroviruses encoding four pluripotency factors (SOX2, KLF4, c-MYC and OCT4). These differentiated cells can be used in disease models (such as progeria) for studying the molecular basis of a broad range of human diseases that are otherwise difficult to study. (credit: Yamanaka S. et al./Nature)

The scientists did that by inducing (modifying) the expression of four specific “epigenetic marks” called “Yamanaka factors” in the iPS cells, with the goal of allowing the cells to grow into adult cells without defects.

Researchers have previously done that successfully with cells in vitro (in a test tube), allowing these factors to be expressed for the needed 2 to 3 weeks for cells. But when they tried that in vivo (in live mice), it resulted in mice that later either died immediately or developed extensive tumors.

Partial cellular reprogramming with the four Yamanaka factors (Oct4, Sox2, Klf4, c-Myc) erases cellular markers of aging in progeria mouse cells (credit: Alejandro Ocampo et al./Cell)

So instead, the Salk team used partial in vivo cellular reprogramming. They induced expression of Yamanaka factors for just 2 to 4 days instead of 2 to 3 weeks. Instead of resulting in tumors or death, that prolonged the mice lifespan. An in vitro experiment also showed reduced DNA damage accumulation and restored nuclear structure.

This image depicts the discovery by Salk Institute researchers that partial cellular reprogramming reversed cellular signs of aging such as accumulation of DNA damage. (Left) Progeria mouse fibroblast cells; (Right) Progeria mouse fibroblast cells rejuvinated by partial reprogramming. (credit: Juan Carlos Izpisua Belmonte Lab/Salk Institute)

“These changes are the result of epigenetic remodeling in the cell,” notes lead investigator Juan Carlos Izpisua Belmonte, a professor in the Salk Institute of Biological Science’s Gene Expression Laboratory.

Several organs improved. For instance, tissue from skin, spleen, kidney and stomach all had improved appearance when inspected under the microscope. The cardiovascular system, which often fails and causes early death in these prematurely aging mice, also showed improvements in structure and function.

This image shows the discovery by researchers that induction of partial cellular reprogramming improved muscle regeneration in aged mice. (Left) Impaired muscle repair in aged mice; (Right) Improved muscle regeneration in aged mice subjected to reprogramming. (credit: Juan Carlos Izpisua Belmonte Lab/Salk Institute)

The team also tested partial reprogramming in mouse models that had injury, resulting in enhanced regeneration of muscle tissue and pancreas beta cells (which store and release insulin).

Next steps will involve learning more about how the epigenome changes during partial reprogramming. “We need to go back and explore which marks are changing and driving the aging process,” says Belmonte.

This study was supported by the G. Harold and Leila Y. Mathers Charitable Foundation, The Leona M. and Harry B. Helmsley Charitable Trust, The Glenn Foundation, Universidad Católica San Antonio de Murcia (UCAM), and Fundación Dr. Pedro Guillen.

* Mice do not perfectly mimic human aging. Researchers generate and use mouse models of premature aging by introducing mutations responsible for these human diseases in mouse.

** Epigenetic marks in the DNA regulate and protect the genome. Some marks turn on specialized functions, such as skin cell machinery in a skin cell; others turn off mechanisms that aren’t needed, such as liver cell machinery in the skin. They are modified over a lifetime in response to environmental changes, and have been proposed as drivers of aging.

*** Induced pluripotent stem cells (iPS cells or iPSCs) are a type of pluripotent stem cell that can be generated directly from adult cells. The iPSC technology was pioneered by Shinya Yamanaka’s lab in Kyoto, Japan, who showed in 2006 that the introduction of four specific genes encoding transcription factors could convert adult cells into pluripotent stem cells. He was awarded the 2012 Nobel Prize in Physiology or Medicine with Sir John Gurdon.

Salk Institute | Salk scientists reverse signs of aging in mice

Abstract of In Vivo Amelioration of Age-Associated Hallmarks by Partial Reprogramming

Aging is the major risk factor for many human diseases. In vitro studies have demonstrated that cellular reprogramming to pluripotency reverses cellular age, but alteration of the aging process through reprogramming has not been directly demonstrated in vivo. Here, we report that partial reprogramming by short-term cyclic expression of Oct4, Sox2, Klf4, and c-Myc (OSKM) ameliorates cellular and physiological hallmarks of aging and prolongs lifespan in a mouse model of premature aging. Similarly, expression of OSKM in vivo improves recovery from metabolic disease and muscle injury in older wild-type mice. The amelioration of age-associated phenotypes by epigenetic remodeling during cellular reprogramming highlights the role of epigenetic dysregulation as a driver of mammalian aging. Establishing in vivo platforms to modulate age-associated epigenetic marks may provide further insights into the biology of aging.

Washington State University researchers have successfully used a mild electric current to kill drug-resistant bacterial infections, a technology that may eventually be used to treat chronic wound infections. Red arrow indicates cell showing a stressed membrane. (credit: Washington State University)

A Washington State University research team has successfully used a mild electric current combined with an antibiotic to kill multidrug-resistant pseudomonas aeruginosa PAO1 bacteria in a lab-cultured biofilm.

These bacteria are responsible for chronic and serious infections in people with lung diseases, such as cystic fibrosis, and in chronic wounds. They also often cause pneumonia for people who are on ventilators and infections in burn victims.*

Schematic of experimental setup for the treatment of biofilm exposed to an e-scaffold, with an illustration of electrochemical production of hydrogen peroxide. The electrodes are connected to a potentiostat (600 mV source; not shown in figure). (credit: Sujala T. Sultana et al./Scientific Reports)

The researchers used an “e-scaffold” (electrochemical structure), a sort of electronic band-aid made out of conductive carbon fabric, which uses an electrical current to produce a low, constant concentration of hydrogen peroxide, an effective disinfectant, at the e-scaffold surface.

The hydrogen peroxide disrupts the biofilm (slime layer) matrix and damages the bacteria cell walls and DNA, which then allows better antibiotic penetration and efficacy against the bacteria. Bacteria that form biofilms are more difficult to kill because antibiotics only partially penetrate this protective layer. Subpopulations of “persister” cells survive treatment and are able to grow and multiply, resulting in chronic infections.

Tuning electrical stimulation to kill bacteria

Researchers have previously tried electrical stimulation, a method used to kill bacteria, for more than a century, but with limited results. In this study, the researchers determined the conditions necessary for the electrochemical reaction to produce hydrogen peroxide. The current has to be carefully controlled to assure the correct reaction at an exact rate to stop the bacteria from developing resistance, while not damaging surrounding tissue.**

The research to develop the e-scaffold actually came out of a failed attempt to improve fuel cells, according to research team leader Haluk Beyenal, the Paul Hohenschuh Distinguished Professor in WSU’s Gene and Linda Voiland School of Chemical Engineering and Bioengineering. When the researchers figured out they could only produce a small amount of electric current for their fuel cell cathode, they decided to see if they could use the process for a different purpose.

The technology may eventually be used to treat chronic wound infections, the researchers say. The researchers have filed a patent application and are working to commercialize the process. They hope to begin conducting clinical tests.

The work, reported in the online edition of npj Biofilms and Microbiomes, was supported by Beyenal’s National Science Foundation CAREER award.

* Bacterial resistance is a growing problem around the world. While antibiotics were a miracle drug of the 20th century, their widespread use has led to drug-resistant strains of bacteria. In the U.S., at least 2 million infections and 23,000 deaths are attributable to antibiotic-resistant bacteria each year, according to the U.S. Centers for Disease Control.

** As the researchers note in the paper, alternative antimicrobial treatments such as silver or mannitol, or in combination with conventional antibiotics, have toxic side effects at adequately high concentrations, and at low concentrations they often decompose before completely eliminating biofilm communities. In addition, persister cells can regrow and form biofilms with potentially enhanced tolerance to antibiotics.

Abstract of Eradication of Pseudomonas aeruginosa biofilms and persister cells using an electrochemical scaffold and enhanced antibiotic susceptibility

Biofilms in chronic wounds are known to contain a persister subpopulation that exhibits enhanced multidrug tolerance and can quickly rebound after therapeutic treatment. The presence of these “persister cells” is partly responsible for the failure of antibiotic therapies and incomplete elimination of biofilms. Electrochemical methods combined with antibiotics have been suggested as an effective alternative for biofilm and persister cell elimination, yet the mechanism of action for improved antibiotic efficacy remains unclear. In this work, an electrochemical scaffold (e-scaffold) that electrochemically generates a constant concentration of H₂O₂ was investigated as a means of enhancing tobramycin susceptibility in pre-grown Pseudomonas aeruginosa PAO1 biofilms and attacking persister cells. Results showed that the e-scaffold enhanced tobramycin susceptibility in P. aeruginosa PAO1 biofilms, which reached a maximum susceptibility at 40 µg/ml tobramycin, with complete elimination (7.8-log reduction vs control biofilm cells, P ≤ 0.001). Moreover, the e-scaffold eradicated persister cells in biofilms, leaving no viable cells (5-log reduction vs control persister cells, P ≤ 0.001). It was observed that the e-scaffold induced the intracellular formation of hydroxyl free radicals and improved membrane permeability in e-scaffold treated biofilm cells, which possibly enhanced antibiotic susceptibility and eradicated persister cells. These results demonstrate a promising advantage of the e-scaffold in the treatment of persistent biofilm infections.

Prolonged preventive antibiotics after surgical incision closure do not prevent infections, but they do change the composition of bacteria in the host at other anatomic locations. The result is resistant colonization of the patient and potentially an infection with Clostridium difficile bacteria, shown here. (credit: CDC)

Overuse and misuse of antimicrobial agents in hospitals is an urgent problem. Surgeons around the world, who often prescribe antibiotics for surgical prophylaxis, need to take a leadership role in promoting “antimicrobial stewardship programs” (ASPs) that can optimize antimicrobial agent use in the hospital.

That’s the message from the Surgical Infection Society and the World Society of Emergency Surgery in an open-access paper entitled “Antimicrobial Stewardship: A  Call to Action for Surgeons,” published in Surgical Infections, a peer-reviewed journal published today (Tuesday, Nov. 15) online ahead of print by Mary Ann Liebert, Inc.*

The authors emphasize the urgent need to standardize the use of antimicrobial agents. Approximately 15% of antibiotic prescribing in hospitals takes place prior to surgery to prevent infection, they note.

(credit: CDC)

The paper is timed to coincide with the CDC’s “Get Smart About Antibiotics Week,” November 14–20, which aims to improve the antibiotic prescribing habits of clinicians to help combat the continuing rise of resistant strains of pathogenic bacteria.

“In addition to emerging resistance, the adverse events of decades of antibiotic use may have led to a number of other adverse consequences,” warns Surgical Infections Editor-in-Chief Donald E. Fry, MD, Northwestern University Feinberg School of Medicine, in an associated open-access editorial, “The Unintended Consequences of Antibiotic Use.”

(credit: CDC)

“The lesson of giving the preventive antibiotics before incision and subsequent contamination has been learned, but the lesson of discontinuation of the antibiotic after the incision has been closed continues to be problematic,” he notes.

“Prolonged preventive antibiotics after incision closure do not prevent infections, but they do change the composition of bacteria in the host at other anatomic locations. The result is resistant colonization of the patient and potentially Clostridium difficile infection. The aggregate effect of prolonged and unnecessary preventive antibiotics is more resistant pathogens in our hospitals.”

Risks of developing antibiotic resistance vs. prevention

A recent KurzweilAI news article reports that an international research team has developed a new antimicrobial peptide, clavanin-MO, that kills strains resistant to existing antibiotics. The researchers advised that the peptide could also be embedded in surfaces such as tabletops to make them resistant to microbial growth, as antimicrobial coatings for catheters, and in ointments to treat skin infections. Two KurzweilAI readers (“tedhowardnz” and “DevilDocNowCiv”) questioned this advice, suggesting that we need to minimize exposure to prevent antibiotic resistance.

One of the senior authors of the associated paper, César de la Fuente Nunez, has replied: “I agree exposure should be limited and regulated. Over-exposure and misuse of conventional antibiotics is one of the main reason bacteria have developed resistance to these drugs. However, it has recently been estimated that if we don’t develop novel therapies, drug-resistant infections will kill 10 million people annually, which corresponds to 1 death every 3 seconds. [We] need to come up with alternative strategies to treat these infections [that have] driven much of our research, including this study.

“Interestingly, work by others has shown that peptides, similar to the ones we have described here, do not readily select for resistance, particularly when compared to conventional antibiotics. We believe this is due to their multifunctional mechanism of action (i.e., they have multiple targets). We envision these peptides being used in adjuvant therapies with antibiotics, as they can potentiate antibiotic action, therefore reducing levels of both peptide and antibiotics required for effective treatment. This approach will help further reduce selective pressure towards the development of resistance.

“Hospital procedures currently sterilize surfaces using ethanol, etc. We think these peptides could be useful, for instance, to coat catheters to prevent microbial colonization. Catheters are often infected, meaning the patient has to undergo surgery to replace the catheter, with all the costs that are associated with this procedure. We think peptides may help prevent some of these infections.”

In related news …

• A multi-drug resistant mycobacteria lung infection (Mycobacterium abscessus) that can cause life-threatening illness in people with cystic fibrosis (CF) and can spread from patient to patient has now spread globally and is becoming increasingly virulent, according to new research published November 11 in the journal Science. The mystery: how does the pathogen manage to spread globally? The researchers speculate that healthy individuals may be unwittingly carrying the mycobacteria between countries, possibly via fomites (carriers, such as a dish or an article of clothing) and aerosols (particles dispersed in air or a gas).
• A previously unnoticed global outbreak of Mycobacterium chimaera, an invasive, slow-growing bacterium, is linked to heater-cooler devices (HCD) used in cardiac surgery, according to a study published Nov. 14 in Infection Control & Hospital Epidemiology. HCDs are stand-alone devices needed for heat exchange in heart-lung machines used in some 250,000 surgeries annually in the U.S., according to the CDC.
• Symptom-free Ebola infections have been found by researchers in 14 individuals in Sierra Leone, West Africa, who showed no signs of Ebola but have evidence of prior Ebola infection in their immune systems. (This open-access link to a PLOS Neglected Tropical Diseases paper goes live upon publication.)

* Coauthored by Senior author John E. Mazuski, MD; Massimo Sartelli, Macerata Hospital (Italy); and colleagues from John Peter Smith Health Network (Fort Worth, TX), Maggiore Hospital (Parma, Italy), Papa XXIII (Bergamo, Italy), University of Texas Health Science Center (Houston), UNIVPM (Ancona, Italy), Vanderbilt University Medical Center (Nashville, TN), and Washington University School of Medicine (St. Louis, MO). Mazuski has received research support from Astra-Zeneca, Bayer, and Merck, and honoraria as an advisory board member, consultant, or speaker from Allergan, Astra-Zeneca, Bayer, and Merck. Mazuski also receives grant support from the National Institutes of Health for collaborative work on an infection control research project. He serves as the President of the Surgical Infection Society without compensation. For the remaining authors, no competing financial interests exist.

Abstract of Antimicrobial Stewardship: A Call to Action for Surgeons

Scanning electron micrograph (SEM) showing a strain of Staphylococcus aureus bacteria taken from a vancomycin intermediate resistant culture (credit: CDC)

A team of researchers at MIT, the University of Brasilia, and the University of British Columbia has engineered an antimicrobial peptide to wipe out many types of bacteria, including some that are resistant to most antibiotics.

A recent study from a U.K. commission on antimicrobial resistance estimated that by 2050, antibiotic-resistant bacterial infections will kill 10 million people per year if no new drugs are developed.

Learning from nature

Living organisms naturally make antimicrobial peptides, as part of their immune system, to kill bacteria, as well as other persistent microbes such as viruses and fungi. It’s done by poking holes in the invaders’ cell membranes. Once inside, they can disrupt several cellular targets, including DNA, RNA, and proteins.

What also sets antimicrobial peptides apart from traditional antibiotics is their ability to recruit the host’s immune system, summoning cells called leukocytes that secrete chemicals that help kill the invading microbes.

In this new study, which appears in the Nov. 2 issue of Nature’s (open-access) Scientific Reports, the researchers began with a naturally occurring antimicrobial peptide called clavanin-A, which has proven deadly to many bacterial strains. The researchers decided to try to engineer it to make it even more effective.*

Killing resistant strains of E. coli and Staph

A microscopic image of E. coli bacteria (credit: A*STAR Institute of Bioengineering and Nanotechnology)

The researchers found in tests with mice that this new peptide, which they called clavanin-MO, could kill strains of Escherichia coli and Staphylococcus aureus that are resistant to most antibiotics.

The researchers also found that the clavanin-MO peptide suppresses the overactive inflammatory response that can cause sepsis, a life threatening condition, and can destroy certain biofilms (persistent thin layers of bacterial cells that form on surfaces). That raises the possibility of using them to treat infections caused by biofilms.**

The clavanin-MO peptide could also be embedded in surfaces such as tabletops to make them resistant to microbial growth, as antimicrobial coatings for catheters, and in ointments to treat skin infections caused by Staphylococcus aureus or other bacteria.

The researchers are now investigating what makes these engineered peptides more effective than the naturally occurring ones, with hopes of further improving them.

* Antimicrobial peptides have a positively charged region that allows them to poke through bacterial cell membranes, and a hydrophobic stretch that enables interaction with and translocation into membranes. The researchers decided to add a sequence of five amino acids that would make the peptides even more hydrophobic, in hopes that it would improve their killing ability.

** Such as the Pseudomonas aeruginosa infections that often affect the lungs of cystic fibrosis patients.

Abstract of An anti-infective synthetic peptide with dual antimicrobial and immunomodulatory activities

Antibiotic-resistant infections are predicted to kill 10 million people per year by 2050, costing the global economy $100 trillion. Therefore, there is an urgent need to develop alternative technologies. We have engineered a synthetic peptide called clavanin-MO, derived from a marine tunicate antimicrobial peptide, which exhibits potent antimicrobial and immunomodulatory properties both in vitro and in vivo. The peptide effectively killed a panel of representative bacterial strains, including multidrug-resistant hospital isolates. Antimicrobial activity of the peptide was demonstrated in animal models, reducing bacterial counts by six orders of magnitude, and contributing to infection clearance. In addition, clavanin-MO was capable of modulating innate immunity by stimulating leukocyte recruitment to the site of infection, and production of immune mediators GM-CSF, IFN-γ and MCP-1, while suppressing an excessive and potentially harmful inflammatory response by increasing synthesis of anti-inflammatory cytokines such as IL-10 and repressing the levels of pro-inflammatory cytokines IL-12 and TNF-α. Finally, treatment with the peptide protected mice against otherwise lethal infections caused by both Gram-negative and -positive drug-resistant strains. The peptide presented here directly kills bacteria and further helps resolve infections through its immune modulatory properties. Peptide anti-infective therapeutics with combined antimicrobial and immunomodulatory properties represent a new approach to treat antibiotic-resistant infections.